| 1 | """ |
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| 2 | Class that holds a fit page state |
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| 3 | """ |
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| 4 | # TODO: Refactor code so we don't need to use getattr/setattr |
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| 5 | ################################################################################ |
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| 6 | # This software was developed by the University of Tennessee as part of the |
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| 7 | # Distributed Data Analysis of Neutron Scattering Experiments (DANSE) |
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| 8 | # project funded by the US National Science Foundation. |
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| 9 | # |
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| 10 | # See the license text in license.txt |
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| 11 | # |
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| 12 | # copyright 2009, University of Tennessee |
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| 13 | ################################################################################ |
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| 14 | import time |
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| 15 | import os |
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| 16 | import sys |
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| 17 | import wx |
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| 18 | import copy |
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| 19 | import logging |
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| 20 | import numpy |
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| 21 | import traceback |
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| 22 | |
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| 23 | import xml.dom.minidom |
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| 24 | from xml.dom.minidom import parseString |
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| 25 | from lxml import etree |
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| 26 | |
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| 27 | from sasmodels import convert |
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| 28 | import sasmodels.weights |
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| 29 | |
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| 30 | import sas.sascalc.dataloader |
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| 31 | from sas.sascalc.dataloader.readers.cansas_reader import Reader as CansasReader |
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| 32 | from sas.sascalc.dataloader.readers.cansas_reader import get_content, write_node |
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| 33 | from sas.sascalc.dataloader.data_info import Data2D, Collimation, Detector |
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| 34 | from sas.sascalc.dataloader.data_info import Process, Aperture |
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| 35 | # Information to read/write state as xml |
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| 36 | FITTING_NODE_NAME = 'fitting_plug_in' |
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| 37 | CANSAS_NS = "cansas1d/1.0" |
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| 38 | |
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| 39 | LIST_OF_DATA_ATTRIBUTES = [["is_data", "is_data", "bool"], |
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| 40 | ["group_id", "data_group_id", "string"], |
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| 41 | ["data_name", "data_name", "string"], |
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| 42 | ["data_id", "data_id", "string"], |
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| 43 | ["name", "name", "string"], |
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| 44 | ["data_name", "data_name", "string"]] |
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| 45 | LIST_OF_STATE_ATTRIBUTES = [["qmin", "qmin", "float"], |
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| 46 | ["qmax", "qmax", "float"], |
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| 47 | ["npts", "npts", "float"], |
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| 48 | ["categorycombobox", "categorycombobox", "string"], |
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| 49 | ["formfactorcombobox", "formfactorcombobox", |
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| 50 | "string"], |
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| 51 | ["structurecombobox", "structurecombobox", |
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| 52 | "string"], |
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| 53 | ["multi_factor", "multi_factor", "float"], |
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| 54 | ["magnetic_on", "magnetic_on", "bool"], |
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| 55 | ["enable_smearer", "enable_smearer", "bool"], |
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| 56 | ["disable_smearer", "disable_smearer", "bool"], |
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| 57 | ["pinhole_smearer", "pinhole_smearer", "bool"], |
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| 58 | ["slit_smearer", "slit_smearer", "bool"], |
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| 59 | ["enable_disp", "enable_disp", "bool"], |
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| 60 | ["disable_disp", "disable_disp", "bool"], |
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| 61 | ["dI_noweight", "dI_noweight", "bool"], |
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| 62 | ["dI_didata", "dI_didata", "bool"], |
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| 63 | ["dI_sqrdata", "dI_sqrdata", "bool"], |
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| 64 | ["dI_idata", "dI_idata", "bool"], |
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| 65 | ["enable2D", "enable2D", "bool"], |
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| 66 | ["cb1", "cb1", "bool"], |
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| 67 | ["tcChi", "tcChi", "float"], |
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| 68 | ["smearer", "smearer", "float"], |
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| 69 | ["smear_type", "smear_type", "string"], |
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| 70 | ["dq_l", "dq_l", "float"], |
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| 71 | ["dq_r", "dq_r", "float"], |
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| 72 | ["dx_max", "dx_max", "float"], |
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| 73 | ["dx_min", "dx_min", "float"], |
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| 74 | ["dxl", "dxl", "float"], |
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| 75 | ["dxw", "dxw", "float"]] |
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| 76 | |
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| 77 | LIST_OF_MODEL_ATTRIBUTES = [["values", "values"], |
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| 78 | ["weights", "weights"]] |
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| 79 | |
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| 80 | DISPERSION_LIST = [["disp_obj_dict", "_disp_obj_dict", "string"]] |
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| 81 | |
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| 82 | LIST_OF_STATE_PARAMETERS = [["parameters", "parameters"], |
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| 83 | ["str_parameters", "str_parameters"], |
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| 84 | ["orientation_parameters", "orientation_params"], |
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| 85 | ["dispersity_parameters", |
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| 86 | "orientation_params_disp"], |
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| 87 | ["fixed_param", "fixed_param"], |
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| 88 | ["fittable_param", "fittable_param"]] |
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| 89 | LIST_OF_DATA_2D_ATTR = [["xmin", "xmin", "float"], |
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| 90 | ["xmax", "xmax", "float"], |
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| 91 | ["ymin", "ymin", "float"], |
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| 92 | ["ymax", "ymax", "float"], |
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| 93 | ["_xaxis", "_xaxis", "string"], |
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| 94 | ["_xunit", "_xunit", "string"], |
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| 95 | ["_yaxis", "_yaxis", "string"], |
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| 96 | ["_yunit", "_yunit", "string"], |
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| 97 | ["_zaxis", "_zaxis", "string"], |
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| 98 | ["_zunit", "_zunit", "string"]] |
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| 99 | LIST_OF_DATA_2D_VALUES = [["qx_data", "qx_data", "float"], |
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| 100 | ["qy_data", "qy_data", "float"], |
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| 101 | ["dqx_data", "dqx_data", "float"], |
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| 102 | ["dqy_data", "dqy_data", "float"], |
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| 103 | ["data", "data", "float"], |
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| 104 | ["q_data", "q_data", "float"], |
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| 105 | ["err_data", "err_data", "float"], |
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| 106 | ["mask", "mask", "bool"]] |
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| 107 | |
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| 108 | |
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| 109 | def parse_entry_helper(node, item): |
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| 110 | """ |
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| 111 | Create a numpy list from value extrated from the node |
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| 112 | |
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| 113 | :param node: node from each the value is stored |
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| 114 | :param item: list name of three strings.the two first are name of data |
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| 115 | attribute and the third one is the type of the value of that |
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| 116 | attribute. type can be string, float, bool, etc. |
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| 117 | |
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| 118 | : return: numpy array |
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| 119 | """ |
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| 120 | if node is not None: |
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| 121 | if item[2] == "string": |
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| 122 | return str(node.get(item[0]).strip()) |
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| 123 | elif item[2] == "bool": |
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| 124 | try: |
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| 125 | return node.get(item[0]).strip() == "True" |
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| 126 | except Exception: |
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| 127 | return None |
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| 128 | else: |
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| 129 | try: |
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| 130 | return float(node.get(item[0])) |
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| 131 | except Exception: |
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| 132 | return None |
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| 133 | |
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| 134 | |
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| 135 | class PageState(object): |
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| 136 | """ |
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| 137 | Contains information to reconstruct a page of the fitpanel. |
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| 138 | """ |
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| 139 | def __init__(self, parent=None, model=None, data=None): |
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| 140 | """ |
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| 141 | Initialize the current state |
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| 142 | |
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| 143 | :param model: a selected model within a page |
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| 144 | :param data: |
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| 145 | |
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| 146 | """ |
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| 147 | self.file = None |
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| 148 | # Time of state creation |
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| 149 | self.timestamp = time.time() |
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| 150 | # Data member to store the dispersion object created |
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| 151 | self._disp_obj_dict = {} |
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| 152 | # ------------------------ |
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| 153 | # Data used for fitting |
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| 154 | self.data = data |
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| 155 | # model data |
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| 156 | self.theory_data = None |
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| 157 | # Is 2D |
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| 158 | self.is_2D = False |
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| 159 | self.images = None |
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| 160 | |
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| 161 | # save additional information on data that dataloader.reader |
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| 162 | # does not read |
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| 163 | self.is_data = None |
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| 164 | self.data_name = "" |
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| 165 | |
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| 166 | if self.data is not None: |
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| 167 | self.data_name = self.data.name |
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| 168 | self.data_id = None |
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| 169 | if self.data is not None and hasattr(self.data, "id"): |
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| 170 | self.data_id = self.data.id |
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| 171 | self.data_group_id = None |
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| 172 | if self.data is not None and hasattr(self.data, "group_id"): |
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| 173 | self.data_group_id = self.data.group_id |
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| 174 | |
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| 175 | # reset True change the state of existing button |
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| 176 | self.reset = False |
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| 177 | |
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| 178 | # flag to allow data2D plot |
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| 179 | self.enable2D = False |
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| 180 | # model on which the fit would be performed |
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| 181 | self.model = model |
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| 182 | self.m_name = None |
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| 183 | # list of process done to model |
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| 184 | self.process = [] |
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| 185 | # fit page manager |
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| 186 | self.manager = None |
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| 187 | # Store the parent of this panel parent |
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| 188 | # For this application fitpanel is the parent |
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| 189 | self.parent = parent |
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| 190 | # Event_owner is the owner of model event |
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| 191 | self.event_owner = None |
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| 192 | # page name |
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| 193 | self.page_name = "" |
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| 194 | # Contains link between model, its parameters, and panel organization |
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| 195 | self.parameters = [] |
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| 196 | # String parameter list that can not be fitted |
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| 197 | self.str_parameters = [] |
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| 198 | # Contains list of parameters that cannot be fitted and reference to |
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| 199 | # panel objects |
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| 200 | self.fixed_param = [] |
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| 201 | # Contains list of parameters with dispersity and reference to |
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| 202 | # panel objects |
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| 203 | self.fittable_param = [] |
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| 204 | # orientation parameters |
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| 205 | self.orientation_params = [] |
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| 206 | # orientation parameters for gaussian dispersity |
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| 207 | self.orientation_params_disp = [] |
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| 208 | # smearer info |
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| 209 | self.smearer = None |
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| 210 | self.smear_type = None |
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| 211 | self.dq_l = None |
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| 212 | self.dq_r = None |
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| 213 | self.dx_max = None |
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| 214 | self.dx_min = None |
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| 215 | self.dxl = None |
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| 216 | self.dxw = None |
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| 217 | # list of dispersion parameters |
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| 218 | self.disp_list = [] |
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| 219 | if self.model is not None: |
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| 220 | self.disp_list = self.model.getDispParamList() |
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| 221 | |
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| 222 | self.disp_cb_dict = {} |
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| 223 | self.values = {} |
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| 224 | self.weights = {} |
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| 225 | |
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| 226 | # contains link between a model and selected parameters to fit |
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| 227 | self.param_toFit = [] |
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| 228 | # dictionary of model type and model class |
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| 229 | self.model_list_box = None |
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| 230 | # save the state of the context menu |
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| 231 | self.saved_states = {} |
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| 232 | # save selection of combobox |
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| 233 | self.formfactorcombobox = None |
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| 234 | self.categorycombobox = None |
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| 235 | self.structurecombobox = None |
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| 236 | |
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| 237 | # radio box to select type of model |
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| 238 | # self.shape_rbutton = False |
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| 239 | # self.shape_indep_rbutton = False |
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| 240 | # self.struct_rbutton = False |
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| 241 | # self.plugin_rbutton = False |
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| 242 | # the indice of the current selection |
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| 243 | self.disp_box = 0 |
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| 244 | # Qrange |
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| 245 | # Q range |
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| 246 | self.qmin = 0.001 |
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| 247 | self.qmax = 0.1 |
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| 248 | # reset data range |
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| 249 | self.qmax_x = None |
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| 250 | self.qmin_x = None |
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| 251 | |
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| 252 | self.npts = None |
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| 253 | self.name = "" |
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| 254 | self.multi_factor = None |
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| 255 | self.magnetic_on = False |
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| 256 | # enable smearering state |
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| 257 | self.enable_smearer = False |
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| 258 | self.disable_smearer = True |
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| 259 | self.pinhole_smearer = False |
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| 260 | self.slit_smearer = False |
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| 261 | # weighting options |
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| 262 | self.dI_noweight = False |
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| 263 | self.dI_didata = True |
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| 264 | self.dI_sqrdata = False |
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| 265 | self.dI_idata = False |
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| 266 | # disperity selection |
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| 267 | self.enable_disp = False |
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| 268 | self.disable_disp = True |
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| 269 | |
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| 270 | # state of selected all check button |
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| 271 | self.cb1 = False |
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| 272 | # store value of chisqr |
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| 273 | self.tcChi = None |
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| 274 | self.version = (1,0,0) |
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| 275 | |
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| 276 | def clone(self): |
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| 277 | """ |
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| 278 | Create a new copy of the current object |
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| 279 | """ |
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| 280 | model = None |
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| 281 | if self.model is not None: |
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| 282 | model = self.model.clone() |
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| 283 | model.name = self.model.name |
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| 284 | obj = PageState(self.parent, model=model) |
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| 285 | obj.file = copy.deepcopy(self.file) |
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| 286 | obj.data = copy.deepcopy(self.data) |
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| 287 | if self.data is not None: |
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| 288 | self.data_name = self.data.name |
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| 289 | obj.data_name = self.data_name |
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| 290 | obj.is_data = self.is_data |
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| 291 | obj.model_list_box = copy.deepcopy(self.model_list_box) |
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| 292 | |
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| 293 | obj.categorycombobox = self.categorycombobox |
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| 294 | obj.formfactorcombobox = self.formfactorcombobox |
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| 295 | obj.structurecombobox = self.structurecombobox |
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| 296 | |
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| 297 | # obj.shape_rbutton = self.shape_rbutton |
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| 298 | # obj.shape_indep_rbutton = self.shape_indep_rbutton |
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| 299 | # obj.struct_rbutton = self.struct_rbutton |
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| 300 | # obj.plugin_rbutton = self.plugin_rbutton |
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| 301 | |
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| 302 | obj.manager = self.manager |
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| 303 | obj.event_owner = self.event_owner |
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| 304 | obj.disp_list = copy.deepcopy(self.disp_list) |
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| 305 | |
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| 306 | obj.enable2D = copy.deepcopy(self.enable2D) |
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| 307 | obj.parameters = copy.deepcopy(self.parameters) |
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| 308 | obj.str_parameters = copy.deepcopy(self.str_parameters) |
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| 309 | obj.fixed_param = copy.deepcopy(self.fixed_param) |
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| 310 | obj.fittable_param = copy.deepcopy(self.fittable_param) |
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| 311 | obj.orientation_params = copy.deepcopy(self.orientation_params) |
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| 312 | obj.orientation_params_disp = \ |
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| 313 | copy.deepcopy(self.orientation_params_disp) |
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| 314 | obj.enable_disp = copy.deepcopy(self.enable_disp) |
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| 315 | obj.disable_disp = copy.deepcopy(self.disable_disp) |
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| 316 | obj.tcChi = self.tcChi |
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| 317 | |
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| 318 | if len(self._disp_obj_dict) > 0: |
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| 319 | for k, v in self._disp_obj_dict.iteritems(): |
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| 320 | obj._disp_obj_dict[k] = v |
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| 321 | if len(self.disp_cb_dict) > 0: |
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| 322 | for k, v in self.disp_cb_dict.iteritems(): |
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| 323 | obj.disp_cb_dict[k] = v |
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| 324 | if len(self.values) > 0: |
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| 325 | for k, v in self.values.iteritems(): |
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| 326 | obj.values[k] = v |
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| 327 | if len(self.weights) > 0: |
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| 328 | for k, v in self.weights.iteritems(): |
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| 329 | obj.weights[k] = v |
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| 330 | obj.enable_smearer = copy.deepcopy(self.enable_smearer) |
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| 331 | obj.disable_smearer = copy.deepcopy(self.disable_smearer) |
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| 332 | obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer) |
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| 333 | obj.slit_smearer = copy.deepcopy(self.slit_smearer) |
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| 334 | obj.smear_type = copy.deepcopy(self.smear_type) |
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| 335 | obj.dI_noweight = copy.deepcopy(self.dI_noweight) |
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| 336 | obj.dI_didata = copy.deepcopy(self.dI_didata) |
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| 337 | obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata) |
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| 338 | obj.dI_idata = copy.deepcopy(self.dI_idata) |
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| 339 | obj.dq_l = copy.deepcopy(self.dq_l) |
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| 340 | obj.dq_r = copy.deepcopy(self.dq_r) |
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| 341 | obj.dx_max = copy.deepcopy(self.dx_max) |
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| 342 | obj.dx_min = copy.deepcopy(self.dx_min) |
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| 343 | obj.dxl = copy.deepcopy(self.dxl) |
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| 344 | obj.dxw = copy.deepcopy(self.dxw) |
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| 345 | obj.disp_box = copy.deepcopy(self.disp_box) |
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| 346 | obj.qmin = copy.deepcopy(self.qmin) |
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| 347 | obj.qmax = copy.deepcopy(self.qmax) |
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| 348 | obj.multi_factor = self.multi_factor |
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| 349 | obj.magnetic_on = self.magnetic_on |
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| 350 | obj.npts = copy.deepcopy(self.npts) |
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| 351 | obj.cb1 = copy.deepcopy(self.cb1) |
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| 352 | obj.smearer = copy.deepcopy(self.smearer) |
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| 353 | |
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| 354 | for name, state in self.saved_states.iteritems(): |
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| 355 | copy_name = copy.deepcopy(name) |
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| 356 | copy_state = state.clone() |
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| 357 | obj.saved_states[copy_name] = copy_state |
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| 358 | return obj |
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| 359 | |
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| 360 | def _old_first_model(self): |
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| 361 | """ |
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| 362 | Handle save states from 4.0.1 and before where the first item in the |
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| 363 | selection boxes of category, formfactor and structurefactor were not |
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| 364 | saved. |
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| 365 | :return: None |
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| 366 | """ |
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| 367 | if self.formfactorcombobox == '': |
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| 368 | if self.categorycombobox == '' and len(self.parameters) == 3: |
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| 369 | self.categorycombobox = "Shape-Independent" |
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| 370 | self.formfactorcombobox = 'PowerLawAbsModel' |
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| 371 | elif self.categorycombobox == '' and len(self.parameters) == 9: |
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| 372 | self.categorycombobox = 'Cylinder' |
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| 373 | self.formfactorcombobox = 'barbell' |
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| 374 | elif self.categorycombobox == 'Shapes': |
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| 375 | self.formfactorcombobox = 'BCCrystalModel' |
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| 376 | elif self.categorycombobox == 'Uncategorized': |
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| 377 | self.formfactorcombobox = 'LineModel' |
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| 378 | elif self.categorycombobox == 'StructureFactor': |
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| 379 | self.structurecombobox = 'HardsphereStructure' |
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| 380 | elif self.categorycombobox == 'Customized Models': |
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| 381 | self.formfactorcombobox = 'MySumFunction' |
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| 382 | elif self.categorycombobox == 'Ellipsoid': |
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| 383 | self.formfactorcombobox = 'core_shell_ellipsoid' |
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| 384 | elif self.categorycombobox == 'Lamellae': |
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| 385 | self.formfactorcombobox = 'lamellar' |
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| 386 | elif self.categorycombobox == 'Paracrystal': |
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| 387 | self.formfactorcombobox = 'bcc_paracrystal' |
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| 388 | elif self.categorycombobox == 'Parallelepiped': |
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| 389 | self.formfactorcombobox = 'core_shell_parallelepiped' |
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| 390 | elif self.categorycombobox == 'Shape Independent': |
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| 391 | self.formfactorcombobox = 'be_polyelectrolyte' |
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| 392 | elif self.categorycombobox == 'Sphere': |
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| 393 | self.formfactorcombobox = 'adsorbed_layer' |
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| 394 | elif self.categorycombobox == 'Structure Factor': |
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| 395 | self.formfactorcombobox = 'hardsphere' |
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| 396 | |
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| 397 | @staticmethod |
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| 398 | def param_remap_to_sasmodels_convert(params, is_string=False): |
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| 399 | """ |
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| 400 | Remaps the parameters for sasmodels conversion |
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| 401 | |
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| 402 | :param params: list of parameters (likely self.parameters) |
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| 403 | :return: remapped dictionary of parameters |
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| 404 | """ |
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| 405 | p = dict() |
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| 406 | for fittable, name, value, _, uncert, lower, upper, units in params: |
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| 407 | if not value: |
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| 408 | value = numpy.nan |
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| 409 | if not uncert or uncert[1] == '' or uncert[1] == 'None': |
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| 410 | uncert[0] = False |
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| 411 | uncert[1] = numpy.nan |
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| 412 | if not upper or upper[1] == '' or upper[1] == 'None': |
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| 413 | upper[0] = False |
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| 414 | upper[1] = numpy.nan |
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| 415 | if not lower or lower[1] == '' or lower[1] == 'None': |
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| 416 | lower[0] = False |
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| 417 | lower[1] = numpy.nan |
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| 418 | if is_string: |
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| 419 | p[name] = str(value) |
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| 420 | else: |
|---|
| 421 | p[name] = float(value) |
|---|
| 422 | p[name + ".fittable"] = bool(fittable) |
|---|
| 423 | p[name + ".std"] = float(uncert[1]) |
|---|
| 424 | p[name + ".upper"] = float(upper[1]) |
|---|
| 425 | p[name + ".lower"] = float(lower[1]) |
|---|
| 426 | p[name + ".units"] = units |
|---|
| 427 | return p |
|---|
| 428 | |
|---|
| 429 | @staticmethod |
|---|
| 430 | def param_remap_from_sasmodels_convert(params): |
|---|
| 431 | """ |
|---|
| 432 | Converts {name : value} map back to [] param list |
|---|
| 433 | :param params: parameter map returned from sasmodels |
|---|
| 434 | :return: None |
|---|
| 435 | """ |
|---|
| 436 | p_map = [] |
|---|
| 437 | for name, info in params.iteritems(): |
|---|
| 438 | if ".fittable" in name or ".std" in name or ".upper" in name or \ |
|---|
| 439 | ".lower" in name or ".units" in name: |
|---|
| 440 | pass |
|---|
| 441 | else: |
|---|
| 442 | fittable = params.get(name + ".fittable", True) |
|---|
| 443 | std = params.get(name + ".std", '0.0') |
|---|
| 444 | upper = params.get(name + ".upper", 'inf') |
|---|
| 445 | lower = params.get(name + ".lower", '-inf') |
|---|
| 446 | units = params.get(name + ".units") |
|---|
| 447 | if std is not None and std is not numpy.nan: |
|---|
| 448 | std = [True, str(std)] |
|---|
| 449 | else: |
|---|
| 450 | std = [False, ''] |
|---|
| 451 | if lower is not None and lower is not numpy.nan: |
|---|
| 452 | lower = [True, str(lower)] |
|---|
| 453 | else: |
|---|
| 454 | lower = [True, '-inf'] |
|---|
| 455 | if upper is not None and upper is not numpy.nan: |
|---|
| 456 | upper = [True, str(upper)] |
|---|
| 457 | else: |
|---|
| 458 | upper = [True, 'inf'] |
|---|
| 459 | param_list = [bool(fittable), str(name), str(info), |
|---|
| 460 | "+/-", std, lower, upper, str(units)] |
|---|
| 461 | p_map.append(param_list) |
|---|
| 462 | return p_map |
|---|
| 463 | |
|---|
| 464 | def _convert_to_sasmodels(self): |
|---|
| 465 | """ |
|---|
| 466 | Convert parameters to a form usable by sasmodels converter |
|---|
| 467 | |
|---|
| 468 | :return: None |
|---|
| 469 | """ |
|---|
| 470 | # Create conversion dictionary to send to sasmodels |
|---|
| 471 | self._old_first_model() |
|---|
| 472 | p = self.param_remap_to_sasmodels_convert(self.parameters) |
|---|
| 473 | structurefactor, params = convert.convert_model(self.structurecombobox, |
|---|
| 474 | p, False, self.version) |
|---|
| 475 | formfactor, params = convert.convert_model(self.formfactorcombobox, |
|---|
| 476 | params, False, self.version) |
|---|
| 477 | if len(self.str_parameters) > 0: |
|---|
| 478 | str_pars = self.param_remap_to_sasmodels_convert( |
|---|
| 479 | self.str_parameters, True) |
|---|
| 480 | formfactor, str_params = convert.convert_model( |
|---|
| 481 | self.formfactorcombobox, str_pars) |
|---|
| 482 | for key, value in str_params.iteritems(): |
|---|
| 483 | params[key] = value |
|---|
| 484 | |
|---|
| 485 | # Only convert if old != new, otherwise all the same |
|---|
| 486 | if formfactor != self.formfactorcombobox or \ |
|---|
| 487 | structurefactor != self.structurecombobox: |
|---|
| 488 | # Spherical SLD number of layers changed between 3.1.2 and 4.0 |
|---|
| 489 | if self.formfactorcombobox == 'SphericalSLDModel': |
|---|
| 490 | self.multi_factor += 1 |
|---|
| 491 | self.formfactorcombobox = formfactor |
|---|
| 492 | self.structurecombobox = structurefactor |
|---|
| 493 | self.parameters = [] |
|---|
| 494 | self.parameters = self.param_remap_from_sasmodels_convert(params) |
|---|
| 495 | |
|---|
| 496 | def _repr_helper(self, list, rep): |
|---|
| 497 | """ |
|---|
| 498 | Helper method to print a state |
|---|
| 499 | """ |
|---|
| 500 | for item in list: |
|---|
| 501 | rep += "parameter name: %s \n" % str(item[1]) |
|---|
| 502 | rep += "value: %s\n" % str(item[2]) |
|---|
| 503 | rep += "selected: %s\n" % str(item[0]) |
|---|
| 504 | rep += "error displayed : %s \n" % str(item[4][0]) |
|---|
| 505 | rep += "error value:%s \n" % str(item[4][1]) |
|---|
| 506 | rep += "minimum displayed : %s \n" % str(item[5][0]) |
|---|
| 507 | rep += "minimum value : %s \n" % str(item[5][1]) |
|---|
| 508 | rep += "maximum displayed : %s \n" % str(item[6][0]) |
|---|
| 509 | rep += "maximum value : %s \n" % str(item[6][1]) |
|---|
| 510 | rep += "parameter unit: %s\n\n" % str(item[7]) |
|---|
| 511 | return rep |
|---|
| 512 | |
|---|
| 513 | def __repr__(self): |
|---|
| 514 | """ |
|---|
| 515 | output string for printing |
|---|
| 516 | """ |
|---|
| 517 | rep = "\nState name: %s\n" % self.file |
|---|
| 518 | t = time.localtime(self.timestamp) |
|---|
| 519 | time_str = time.strftime("%b %d %Y %H;%M;%S ", t) |
|---|
| 520 | |
|---|
| 521 | rep += "State created: %s\n" % time_str |
|---|
| 522 | rep += "State form factor combobox selection: %s\n" % \ |
|---|
| 523 | self.formfactorcombobox |
|---|
| 524 | rep += "State structure factor combobox selection: %s\n" % \ |
|---|
| 525 | self.structurecombobox |
|---|
| 526 | rep += "is data : %s\n" % self.is_data |
|---|
| 527 | rep += "data's name : %s\n" % self.data_name |
|---|
| 528 | rep += "data's id : %s\n" % self.data_id |
|---|
| 529 | if self.model is not None: |
|---|
| 530 | m_name = self.model.__class__.__name__ |
|---|
| 531 | if m_name == 'Model': |
|---|
| 532 | m_name = self.m_name |
|---|
| 533 | rep += "model name : %s\n" % m_name |
|---|
| 534 | else: |
|---|
| 535 | rep += "model name : None\n" |
|---|
| 536 | rep += "multi_factor : %s\n" % str(self.multi_factor) |
|---|
| 537 | rep += "magnetic_on : %s\n" % str(self.magnetic_on) |
|---|
| 538 | rep += "model type (Category) selected: %s\n" % self.categorycombobox |
|---|
| 539 | rep += "data : %s\n" % str(self.data) |
|---|
| 540 | rep += "Plotting Range: min: %s, max: %s, steps: %s\n" % \ |
|---|
| 541 | (str(self.qmin), str(self.qmax), str(self.npts)) |
|---|
| 542 | rep += "Dispersion selection : %s\n" % str(self.disp_box) |
|---|
| 543 | rep += "Smearing enable : %s\n" % str(self.enable_smearer) |
|---|
| 544 | rep += "Smearing disable : %s\n" % str(self.disable_smearer) |
|---|
| 545 | rep += "Pinhole smearer enable : %s\n" % str(self.pinhole_smearer) |
|---|
| 546 | rep += "Slit smearer enable : %s\n" % str(self.slit_smearer) |
|---|
| 547 | rep += "Dispersity enable : %s\n" % str(self.enable_disp) |
|---|
| 548 | rep += "Dispersity disable : %s\n" % str(self.disable_disp) |
|---|
| 549 | rep += "Slit smearer enable: %s\n" % str(self.slit_smearer) |
|---|
| 550 | |
|---|
| 551 | rep += "dI_noweight : %s\n" % str(self.dI_noweight) |
|---|
| 552 | rep += "dI_didata : %s\n" % str(self.dI_didata) |
|---|
| 553 | rep += "dI_sqrdata : %s\n" % str(self.dI_sqrdata) |
|---|
| 554 | rep += "dI_idata : %s\n" % str(self.dI_idata) |
|---|
| 555 | |
|---|
| 556 | rep += "2D enable : %s\n" % str(self.enable2D) |
|---|
| 557 | rep += "All parameters checkbox selected: %s\n" % self.cb1 |
|---|
| 558 | rep += "Value of Chisqr : %s\n" % str(self.tcChi) |
|---|
| 559 | rep += "Smear object : %s\n" % self.smearer |
|---|
| 560 | rep += "Smear type : %s\n" % self.smear_type |
|---|
| 561 | rep += "dq_l : %s\n" % self.dq_l |
|---|
| 562 | rep += "dq_r : %s\n" % self.dq_r |
|---|
| 563 | rep += "dx_max : %s\n" % str(self.dx_max) |
|---|
| 564 | rep += "dx_min : %s\n" % str(self.dx_min) |
|---|
| 565 | rep += "dxl : %s\n" % str(self.dxl) |
|---|
| 566 | rep += "dxw : %s\n" % str(self.dxw) |
|---|
| 567 | rep += "model : %s\n\n" % str(self.model) |
|---|
| 568 | temp_parameters = [] |
|---|
| 569 | temp_fittable_param = [] |
|---|
| 570 | if self.data.__class__.__name__ == "Data2D": |
|---|
| 571 | self.is_2D = True |
|---|
| 572 | else: |
|---|
| 573 | self.is_2D = False |
|---|
| 574 | if self.data is not None: |
|---|
| 575 | if not self.is_2D: |
|---|
| 576 | for item in self.parameters: |
|---|
| 577 | if item not in self.orientation_params: |
|---|
| 578 | temp_parameters.append(item) |
|---|
| 579 | for item in self.fittable_param: |
|---|
| 580 | if item not in self.orientation_params_disp: |
|---|
| 581 | temp_fittable_param.append(item) |
|---|
| 582 | else: |
|---|
| 583 | temp_parameters = self.parameters |
|---|
| 584 | temp_fittable_param = self.fittable_param |
|---|
| 585 | |
|---|
| 586 | rep += "number parameters(self.parameters): %s\n" % \ |
|---|
| 587 | len(temp_parameters) |
|---|
| 588 | rep = self._repr_helper(list=temp_parameters, rep=rep) |
|---|
| 589 | rep += "number str_parameters(self.str_parameters): %s\n" % \ |
|---|
| 590 | len(self.str_parameters) |
|---|
| 591 | rep = self._repr_helper(list=self.str_parameters, rep=rep) |
|---|
| 592 | rep += "number fittable_param(self.fittable_param): %s\n" % \ |
|---|
| 593 | len(temp_fittable_param) |
|---|
| 594 | rep = self._repr_helper(list=temp_fittable_param, rep=rep) |
|---|
| 595 | return rep |
|---|
| 596 | |
|---|
| 597 | def set_report_string(self): |
|---|
| 598 | """ |
|---|
| 599 | Get the values (strings) from __str__ for report |
|---|
| 600 | """ |
|---|
| 601 | # Dictionary of the report strings |
|---|
| 602 | repo_time = "" |
|---|
| 603 | model_name = "" |
|---|
| 604 | title = "" |
|---|
| 605 | title_name = "" |
|---|
| 606 | file_name = "" |
|---|
| 607 | param_string = "" |
|---|
| 608 | paramval_string = "" |
|---|
| 609 | chi2_string = "" |
|---|
| 610 | q_range = "" |
|---|
| 611 | strings = self.__repr__() |
|---|
| 612 | lines = strings.split('\n') |
|---|
| 613 | |
|---|
| 614 | # get all string values from __str__() |
|---|
| 615 | for line in lines: |
|---|
| 616 | value = "" |
|---|
| 617 | content = line.split(":") |
|---|
| 618 | name = content[0] |
|---|
| 619 | try: |
|---|
| 620 | value = content[1] |
|---|
| 621 | except Exception: |
|---|
| 622 | msg = "Report string expected 'name: value' but got %r" % line |
|---|
| 623 | logging.error(msg) |
|---|
| 624 | if name.count("State created"): |
|---|
| 625 | repo_time = "" + value |
|---|
| 626 | if name.count("parameter name"): |
|---|
| 627 | val_name = value.split(".") |
|---|
| 628 | if len(val_name) > 1: |
|---|
| 629 | if val_name[1].count("width"): |
|---|
| 630 | param_string += value + ',' |
|---|
| 631 | else: |
|---|
| 632 | continue |
|---|
| 633 | else: |
|---|
| 634 | param_string += value + ',' |
|---|
| 635 | if name == "value": |
|---|
| 636 | param_string += value + ',' |
|---|
| 637 | fixed_parameter = False |
|---|
| 638 | if name == "selected": |
|---|
| 639 | if value == u' False': |
|---|
| 640 | fixed_parameter = True |
|---|
| 641 | if name == "error value": |
|---|
| 642 | if fixed_parameter: |
|---|
| 643 | param_string += '(fixed),' |
|---|
| 644 | else: |
|---|
| 645 | param_string += value + ',' |
|---|
| 646 | if name == "parameter unit": |
|---|
| 647 | param_string += value + ':' |
|---|
| 648 | if name == "Value of Chisqr ": |
|---|
| 649 | chi2 = ("Chi2/Npts = " + value) |
|---|
| 650 | chi2_string = CENTRE % chi2 |
|---|
| 651 | if name == "Title": |
|---|
| 652 | if len(value.strip()) == 0: |
|---|
| 653 | continue |
|---|
| 654 | title = value + " [" + repo_time + "]" |
|---|
| 655 | title_name = HEADER % title |
|---|
| 656 | if name == "data ": |
|---|
| 657 | try: |
|---|
| 658 | file_value = ("File name:" + content[2]) |
|---|
| 659 | file_name = CENTRE % file_value |
|---|
| 660 | if len(title) == 0: |
|---|
| 661 | title = content[2] + " [" + repo_time + "]" |
|---|
| 662 | title_name = HEADER % title |
|---|
| 663 | except Exception: |
|---|
| 664 | msg = "While parsing 'data: ...'\n" |
|---|
| 665 | logging.error(msg + traceback.format_exc()) |
|---|
| 666 | if name == "model name ": |
|---|
| 667 | try: |
|---|
| 668 | modelname = "Model name:" + content[1] |
|---|
| 669 | except: |
|---|
| 670 | modelname = "Model name:" + " NAN" |
|---|
| 671 | model_name = CENTRE % modelname |
|---|
| 672 | |
|---|
| 673 | if name == "Plotting Range": |
|---|
| 674 | try: |
|---|
| 675 | q_range = content[1] + " = " + content[2] \ |
|---|
| 676 | + " = " + content[3].split(",")[0] |
|---|
| 677 | q_name = ("Q Range: " + q_range) |
|---|
| 678 | q_range = CENTRE % q_name |
|---|
| 679 | except Exception: |
|---|
| 680 | msg = "While parsing 'Plotting Range: ...'\n" |
|---|
| 681 | logging.error(msg + traceback.format_exc()) |
|---|
| 682 | paramval = "" |
|---|
| 683 | for lines in param_string.split(":"): |
|---|
| 684 | line = lines.split(",") |
|---|
| 685 | if len(lines) > 0: |
|---|
| 686 | param = line[0] |
|---|
| 687 | param += " = " + line[1] |
|---|
| 688 | if len(line[2].split()) > 0 and not line[2].count("None"): |
|---|
| 689 | param += " +- " + line[2] |
|---|
| 690 | if len(line[3].split()) > 0 and not line[3].count("None"): |
|---|
| 691 | param += " " + line[3] |
|---|
| 692 | if not paramval.count(param): |
|---|
| 693 | paramval += param + "\n" |
|---|
| 694 | paramval_string += CENTRE % param + "\n" |
|---|
| 695 | |
|---|
| 696 | text_string = "\n\n\n%s\n\n%s\n%s\n%s\n\n%s" % \ |
|---|
| 697 | (title, file, q_name, chi2, paramval) |
|---|
| 698 | |
|---|
| 699 | title_name = self._check_html_format(title_name) |
|---|
| 700 | file_name = self._check_html_format(file_name) |
|---|
| 701 | title = self._check_html_format(title) |
|---|
| 702 | |
|---|
| 703 | html_string = title_name + "\n" + file_name + \ |
|---|
| 704 | "\n" + model_name + \ |
|---|
| 705 | "\n" + q_range + \ |
|---|
| 706 | "\n" + chi2_string + \ |
|---|
| 707 | "\n" + ELINE + \ |
|---|
| 708 | "\n" + paramval_string + \ |
|---|
| 709 | "\n" + ELINE + \ |
|---|
| 710 | "\n" + FEET_1 % title + \ |
|---|
| 711 | "\n" + FEET_2 |
|---|
| 712 | |
|---|
| 713 | return html_string, text_string, title |
|---|
| 714 | |
|---|
| 715 | def _check_html_format(self, name): |
|---|
| 716 | """ |
|---|
| 717 | Check string '%' for html format |
|---|
| 718 | """ |
|---|
| 719 | if name.count('%'): |
|---|
| 720 | name = name.replace('%', '%') |
|---|
| 721 | |
|---|
| 722 | return name |
|---|
| 723 | |
|---|
| 724 | def report(self, figs=None, canvases=None): |
|---|
| 725 | """ |
|---|
| 726 | Invoke report dialog panel |
|---|
| 727 | |
|---|
| 728 | : param figs: list of pylab figures [list] |
|---|
| 729 | """ |
|---|
| 730 | from sas.sasgui.perspectives.fitting.report_dialog import ReportDialog |
|---|
| 731 | # get the strings for report |
|---|
| 732 | html_str, text_str, title = self.set_report_string() |
|---|
| 733 | # Allow 2 figures to append |
|---|
| 734 | if len(figs) == 1: |
|---|
| 735 | add_str = FEET_3 |
|---|
| 736 | elif len(figs) == 2: |
|---|
| 737 | add_str = ELINE |
|---|
| 738 | add_str += FEET_2 % ("%s") |
|---|
| 739 | add_str += ELINE |
|---|
| 740 | add_str += FEET_3 |
|---|
| 741 | elif len(figs) > 2: |
|---|
| 742 | add_str = ELINE |
|---|
| 743 | add_str += FEET_2 % ("%s") |
|---|
| 744 | add_str += ELINE |
|---|
| 745 | add_str += FEET_2 % ("%s") |
|---|
| 746 | add_str += ELINE |
|---|
| 747 | add_str += FEET_3 |
|---|
| 748 | else: |
|---|
| 749 | add_str = "" |
|---|
| 750 | |
|---|
| 751 | # final report html strings |
|---|
| 752 | report_str = html_str % ("%s") + add_str |
|---|
| 753 | |
|---|
| 754 | # make plot image |
|---|
| 755 | images = self.set_plot_state(figs, canvases) |
|---|
| 756 | report_list = [report_str, text_str, images] |
|---|
| 757 | dialog = ReportDialog(report_list, None, wx.ID_ANY, "") |
|---|
| 758 | dialog.Show() |
|---|
| 759 | |
|---|
| 760 | def _to_xml_helper(self, thelist, element, newdoc): |
|---|
| 761 | """ |
|---|
| 762 | Helper method to create xml file for saving state |
|---|
| 763 | """ |
|---|
| 764 | for item in thelist: |
|---|
| 765 | sub_element = newdoc.createElement('parameter') |
|---|
| 766 | sub_element.setAttribute('name', str(item[1])) |
|---|
| 767 | sub_element.setAttribute('value', str(item[2])) |
|---|
| 768 | sub_element.setAttribute('selected_to_fit', str(item[0])) |
|---|
| 769 | sub_element.setAttribute('error_displayed', str(item[4][0])) |
|---|
| 770 | sub_element.setAttribute('error_value', str(item[4][1])) |
|---|
| 771 | sub_element.setAttribute('minimum_displayed', str(item[5][0])) |
|---|
| 772 | sub_element.setAttribute('minimum_value', str(item[5][1])) |
|---|
| 773 | sub_element.setAttribute('maximum_displayed', str(item[6][0])) |
|---|
| 774 | sub_element.setAttribute('maximum_value', str(item[6][1])) |
|---|
| 775 | sub_element.setAttribute('unit', str(item[7])) |
|---|
| 776 | element.appendChild(sub_element) |
|---|
| 777 | |
|---|
| 778 | def to_xml(self, file="fitting_state.fitv", doc=None, |
|---|
| 779 | entry_node=None, batch_fit_state=None): |
|---|
| 780 | """ |
|---|
| 781 | Writes the state of the fit panel to file, as XML. |
|---|
| 782 | |
|---|
| 783 | Compatible with standalone writing, or appending to an |
|---|
| 784 | already existing XML document. In that case, the XML document is |
|---|
| 785 | required. An optional entry node in the XML document may also be given. |
|---|
| 786 | |
|---|
| 787 | :param file: file to write to |
|---|
| 788 | :param doc: XML document object [optional] |
|---|
| 789 | :param entry_node: XML node within the XML document at which we |
|---|
| 790 | will append the data [optional] |
|---|
| 791 | :param batch_fit_state: simultaneous fit state |
|---|
| 792 | """ |
|---|
| 793 | from xml.dom.minidom import getDOMImplementation |
|---|
| 794 | |
|---|
| 795 | # Check whether we have to write a standalone XML file |
|---|
| 796 | if doc is None: |
|---|
| 797 | impl = getDOMImplementation() |
|---|
| 798 | doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0") |
|---|
| 799 | newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type) |
|---|
| 800 | top_element = newdoc.documentElement |
|---|
| 801 | else: |
|---|
| 802 | # We are appending to an existing document |
|---|
| 803 | newdoc = doc |
|---|
| 804 | try: |
|---|
| 805 | top_element = newdoc.createElement(FITTING_NODE_NAME) |
|---|
| 806 | except: |
|---|
| 807 | string = etree.tostring(doc, pretty_print=True) |
|---|
| 808 | newdoc = parseString(string) |
|---|
| 809 | top_element = newdoc.createElement(FITTING_NODE_NAME) |
|---|
| 810 | if entry_node is None: |
|---|
| 811 | newdoc.documentElement.appendChild(top_element) |
|---|
| 812 | else: |
|---|
| 813 | try: |
|---|
| 814 | entry_node.appendChild(top_element) |
|---|
| 815 | except: |
|---|
| 816 | node_name = entry_node.tag |
|---|
| 817 | node_list = newdoc.getElementsByTagName(node_name) |
|---|
| 818 | entry_node = node_list.item(0) |
|---|
| 819 | entry_node.appendChild(top_element) |
|---|
| 820 | |
|---|
| 821 | attr = newdoc.createAttribute("version") |
|---|
| 822 | import sasview |
|---|
| 823 | attr.nodeValue = sasview.__version__ |
|---|
| 824 | # attr.nodeValue = '1.0' |
|---|
| 825 | top_element.setAttributeNode(attr) |
|---|
| 826 | |
|---|
| 827 | # File name |
|---|
| 828 | element = newdoc.createElement("filename") |
|---|
| 829 | if self.file is not None: |
|---|
| 830 | element.appendChild(newdoc.createTextNode(str(self.file))) |
|---|
| 831 | else: |
|---|
| 832 | element.appendChild(newdoc.createTextNode(str(file))) |
|---|
| 833 | top_element.appendChild(element) |
|---|
| 834 | |
|---|
| 835 | element = newdoc.createElement("timestamp") |
|---|
| 836 | element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp))) |
|---|
| 837 | attr = newdoc.createAttribute("epoch") |
|---|
| 838 | attr.nodeValue = str(self.timestamp) |
|---|
| 839 | element.setAttributeNode(attr) |
|---|
| 840 | top_element.appendChild(element) |
|---|
| 841 | |
|---|
| 842 | # Inputs |
|---|
| 843 | inputs = newdoc.createElement("Attributes") |
|---|
| 844 | top_element.appendChild(inputs) |
|---|
| 845 | |
|---|
| 846 | if self.data is not None and hasattr(self.data, "group_id"): |
|---|
| 847 | self.data_group_id = self.data.group_id |
|---|
| 848 | if self.data is not None and hasattr(self.data, "is_data"): |
|---|
| 849 | self.is_data = self.data.is_data |
|---|
| 850 | if self.data is not None: |
|---|
| 851 | self.data_name = self.data.name |
|---|
| 852 | if self.data is not None and hasattr(self.data, "id"): |
|---|
| 853 | self.data_id = self.data.id |
|---|
| 854 | |
|---|
| 855 | for item in LIST_OF_DATA_ATTRIBUTES: |
|---|
| 856 | element = newdoc.createElement(item[0]) |
|---|
| 857 | element.setAttribute(item[0], str(getattr(self, item[1]))) |
|---|
| 858 | inputs.appendChild(element) |
|---|
| 859 | |
|---|
| 860 | for item in LIST_OF_STATE_ATTRIBUTES: |
|---|
| 861 | element = newdoc.createElement(item[0]) |
|---|
| 862 | element.setAttribute(item[0], str(getattr(self, item[1]))) |
|---|
| 863 | inputs.appendChild(element) |
|---|
| 864 | |
|---|
| 865 | # For self.values ={ disp_param_name: [vals,...],...} |
|---|
| 866 | # and for self.weights ={ disp_param_name: [weights,...],...} |
|---|
| 867 | for item in LIST_OF_MODEL_ATTRIBUTES: |
|---|
| 868 | element = newdoc.createElement(item[0]) |
|---|
| 869 | value_list = getattr(self, item[1]) |
|---|
| 870 | for key, value in value_list.iteritems(): |
|---|
| 871 | sub_element = newdoc.createElement(key) |
|---|
| 872 | sub_element.setAttribute('name', str(key)) |
|---|
| 873 | for val in value: |
|---|
| 874 | sub_element.appendChild(newdoc.createTextNode(str(val))) |
|---|
| 875 | |
|---|
| 876 | element.appendChild(sub_element) |
|---|
| 877 | inputs.appendChild(element) |
|---|
| 878 | |
|---|
| 879 | # Create doc for the dictionary of self._disp_obj_dic |
|---|
| 880 | for tagname, varname, tagtype in DISPERSION_LIST: |
|---|
| 881 | element = newdoc.createElement(tagname) |
|---|
| 882 | value_list = getattr(self, varname) |
|---|
| 883 | for key, value in value_list.iteritems(): |
|---|
| 884 | sub_element = newdoc.createElement(key) |
|---|
| 885 | sub_element.setAttribute('name', str(key)) |
|---|
| 886 | sub_element.setAttribute('value', str(value)) |
|---|
| 887 | element.appendChild(sub_element) |
|---|
| 888 | inputs.appendChild(element) |
|---|
| 889 | |
|---|
| 890 | for item in LIST_OF_STATE_PARAMETERS: |
|---|
| 891 | element = newdoc.createElement(item[0]) |
|---|
| 892 | self._to_xml_helper(thelist=getattr(self, item[1]), |
|---|
| 893 | element=element, newdoc=newdoc) |
|---|
| 894 | inputs.appendChild(element) |
|---|
| 895 | |
|---|
| 896 | # Combined and Simultaneous Fit Parameters |
|---|
| 897 | if batch_fit_state is not None: |
|---|
| 898 | batch_combo = newdoc.createElement('simultaneous_fit') |
|---|
| 899 | top_element.appendChild(batch_combo) |
|---|
| 900 | |
|---|
| 901 | # Simultaneous Fit Number For Linking Later |
|---|
| 902 | element = newdoc.createElement('sim_fit_number') |
|---|
| 903 | element.setAttribute('fit_number', str(batch_fit_state.fit_page_no)) |
|---|
| 904 | batch_combo.appendChild(element) |
|---|
| 905 | |
|---|
| 906 | # Save constraints |
|---|
| 907 | constraints = newdoc.createElement('constraints') |
|---|
| 908 | batch_combo.appendChild(constraints) |
|---|
| 909 | for constraint in batch_fit_state.constraints_list: |
|---|
| 910 | if constraint.model_cbox.GetValue() != "": |
|---|
| 911 | # model_cbox, param_cbox, egal_txt, constraint, |
|---|
| 912 | # btRemove, sizer |
|---|
| 913 | doc_cons = newdoc.createElement('constraint') |
|---|
| 914 | doc_cons.setAttribute('model_cbox', |
|---|
| 915 | str(constraint.model_cbox.GetValue())) |
|---|
| 916 | doc_cons.setAttribute('param_cbox', |
|---|
| 917 | str(constraint.param_cbox.GetValue())) |
|---|
| 918 | doc_cons.setAttribute('egal_txt', |
|---|
| 919 | str(constraint.egal_txt.GetLabel())) |
|---|
| 920 | doc_cons.setAttribute('constraint', |
|---|
| 921 | str(constraint.constraint.GetValue())) |
|---|
| 922 | constraints.appendChild(doc_cons) |
|---|
| 923 | |
|---|
| 924 | # Save all models |
|---|
| 925 | models = newdoc.createElement('model_list') |
|---|
| 926 | batch_combo.appendChild(models) |
|---|
| 927 | for model in batch_fit_state.model_list: |
|---|
| 928 | doc_model = newdoc.createElement('model_list_item') |
|---|
| 929 | doc_model.setAttribute('checked', str(model[0].GetValue())) |
|---|
| 930 | keys = model[1].keys() |
|---|
| 931 | doc_model.setAttribute('name', str(keys[0])) |
|---|
| 932 | values = model[1].get(keys[0]) |
|---|
| 933 | doc_model.setAttribute('fit_number', str(model[2])) |
|---|
| 934 | doc_model.setAttribute('fit_page_source', str(model[3])) |
|---|
| 935 | doc_model.setAttribute('model_name', str(values.model.id)) |
|---|
| 936 | models.appendChild(doc_model) |
|---|
| 937 | |
|---|
| 938 | # Select All Checkbox |
|---|
| 939 | element = newdoc.createElement('select_all') |
|---|
| 940 | if batch_fit_state.select_all: |
|---|
| 941 | element.setAttribute('checked', 'True') |
|---|
| 942 | else: |
|---|
| 943 | element.setAttribute('checked', 'False') |
|---|
| 944 | batch_combo.appendChild(element) |
|---|
| 945 | |
|---|
| 946 | # Save the file |
|---|
| 947 | if doc is None: |
|---|
| 948 | fd = open(file, 'w') |
|---|
| 949 | fd.write(newdoc.toprettyxml()) |
|---|
| 950 | fd.close() |
|---|
| 951 | return None |
|---|
| 952 | else: |
|---|
| 953 | return newdoc |
|---|
| 954 | |
|---|
| 955 | def _from_xml_helper(self, node, list): |
|---|
| 956 | """ |
|---|
| 957 | Helper function to write state to xml |
|---|
| 958 | """ |
|---|
| 959 | for item in node: |
|---|
| 960 | try: |
|---|
| 961 | name = item.get('name') |
|---|
| 962 | except: |
|---|
| 963 | name = None |
|---|
| 964 | try: |
|---|
| 965 | value = item.get('value') |
|---|
| 966 | except: |
|---|
| 967 | value = None |
|---|
| 968 | try: |
|---|
| 969 | selected_to_fit = (item.get('selected_to_fit') == "True") |
|---|
| 970 | except: |
|---|
| 971 | selected_to_fit = None |
|---|
| 972 | try: |
|---|
| 973 | error_displayed = (item.get('error_displayed') == "True") |
|---|
| 974 | except: |
|---|
| 975 | error_displayed = None |
|---|
| 976 | try: |
|---|
| 977 | error_value = item.get('error_value') |
|---|
| 978 | except: |
|---|
| 979 | error_value = None |
|---|
| 980 | try: |
|---|
| 981 | minimum_displayed = (item.get('minimum_displayed') == "True") |
|---|
| 982 | except: |
|---|
| 983 | minimum_displayed = None |
|---|
| 984 | try: |
|---|
| 985 | minimum_value = item.get('minimum_value') |
|---|
| 986 | except: |
|---|
| 987 | minimum_value = None |
|---|
| 988 | try: |
|---|
| 989 | maximum_displayed = (item.get('maximum_displayed') == "True") |
|---|
| 990 | except: |
|---|
| 991 | maximum_displayed = None |
|---|
| 992 | try: |
|---|
| 993 | maximum_value = item.get('maximum_value') |
|---|
| 994 | except: |
|---|
| 995 | maximum_value = None |
|---|
| 996 | try: |
|---|
| 997 | unit = item.get('unit') |
|---|
| 998 | except: |
|---|
| 999 | unit = None |
|---|
| 1000 | list.append([selected_to_fit, name, value, "+/-", |
|---|
| 1001 | [error_displayed, error_value], |
|---|
| 1002 | [minimum_displayed, minimum_value], |
|---|
| 1003 | [maximum_displayed, maximum_value], unit]) |
|---|
| 1004 | |
|---|
| 1005 | def from_xml(self, file=None, node=None): |
|---|
| 1006 | """ |
|---|
| 1007 | Load fitting state from a file |
|---|
| 1008 | |
|---|
| 1009 | :param file: .fitv file |
|---|
| 1010 | :param node: node of a XML document to read from |
|---|
| 1011 | """ |
|---|
| 1012 | if file is not None: |
|---|
| 1013 | msg = "PageState no longer supports non-CanSAS" |
|---|
| 1014 | msg += " format for fitting files" |
|---|
| 1015 | raise RuntimeError, msg |
|---|
| 1016 | |
|---|
| 1017 | if node.get('version'): |
|---|
| 1018 | |
|---|
| 1019 | self.version = tuple(int(e) for e in |
|---|
| 1020 | str.split(node.get('version'), ".")) |
|---|
| 1021 | # Get file name |
|---|
| 1022 | entry = get_content('ns:filename', node) |
|---|
| 1023 | if entry is not None: |
|---|
| 1024 | self.file = entry.text.strip() |
|---|
| 1025 | |
|---|
| 1026 | # Get time stamp |
|---|
| 1027 | entry = get_content('ns:timestamp', node) |
|---|
| 1028 | if entry is not None and entry.get('epoch'): |
|---|
| 1029 | try: |
|---|
| 1030 | self.timestamp = float(entry.get('epoch')) |
|---|
| 1031 | except: |
|---|
| 1032 | msg = "PageState.fromXML: Could not" |
|---|
| 1033 | msg += " read timestamp\n %s" % sys.exc_value |
|---|
| 1034 | logging.error(msg) |
|---|
| 1035 | |
|---|
| 1036 | if entry is not None: |
|---|
| 1037 | # Parse fitting attributes |
|---|
| 1038 | entry = get_content('ns:Attributes', node) |
|---|
| 1039 | for item in LIST_OF_DATA_ATTRIBUTES: |
|---|
| 1040 | node = get_content('ns:%s' % item[0], entry) |
|---|
| 1041 | setattr(self, item[0], parse_entry_helper(node, item)) |
|---|
| 1042 | |
|---|
| 1043 | for item in LIST_OF_STATE_ATTRIBUTES: |
|---|
| 1044 | node = get_content('ns:%s' % item[0], entry) |
|---|
| 1045 | setattr(self, item[0], parse_entry_helper(node, item)) |
|---|
| 1046 | |
|---|
| 1047 | for item in LIST_OF_STATE_PARAMETERS: |
|---|
| 1048 | node = get_content("ns:%s" % item[0], entry) |
|---|
| 1049 | self._from_xml_helper(node=node, |
|---|
| 1050 | list=getattr(self, item[1])) |
|---|
| 1051 | |
|---|
| 1052 | # Recover _disp_obj_dict from xml file |
|---|
| 1053 | self._disp_obj_dict = {} |
|---|
| 1054 | for tagname, varname, tagtype in DISPERSION_LIST: |
|---|
| 1055 | node = get_content("ns:%s" % tagname, entry) |
|---|
| 1056 | for attr in node: |
|---|
| 1057 | parameter = str(attr.get('name')) |
|---|
| 1058 | value = attr.get('value') |
|---|
| 1059 | if value.startswith("<"): |
|---|
| 1060 | try: |
|---|
| 1061 | # <path.to.NamedDistribution object/instance...> |
|---|
| 1062 | cls_name = value[1:].split()[0].split('.')[-1] |
|---|
| 1063 | cls = getattr(sasmodels.weights, cls_name) |
|---|
| 1064 | value = cls.type |
|---|
| 1065 | except Exception: |
|---|
| 1066 | base = "unable to load distribution %r for %s" |
|---|
| 1067 | logging.error(base % (value, parameter)) |
|---|
| 1068 | continue |
|---|
| 1069 | _disp_obj_dict = getattr(self, varname) |
|---|
| 1070 | _disp_obj_dict[parameter] = value |
|---|
| 1071 | |
|---|
| 1072 | # get self.values and self.weights dic. if exists |
|---|
| 1073 | for tagname, varname in LIST_OF_MODEL_ATTRIBUTES: |
|---|
| 1074 | node = get_content("ns:%s" % tagname, entry) |
|---|
| 1075 | dic = {} |
|---|
| 1076 | value_list = [] |
|---|
| 1077 | for par in node: |
|---|
| 1078 | name = par.get('name') |
|---|
| 1079 | values = par.text.split() |
|---|
| 1080 | # Get lines only with numbers |
|---|
| 1081 | for line in values: |
|---|
| 1082 | try: |
|---|
| 1083 | val = float(line) |
|---|
| 1084 | value_list.append(val) |
|---|
| 1085 | except Exception: |
|---|
| 1086 | # pass if line is empty (it happens) |
|---|
| 1087 | msg = ("Error reading %r from %s %s\n" |
|---|
| 1088 | % (line, tagname, name)) |
|---|
| 1089 | logging.error(msg + traceback.format_exc()) |
|---|
| 1090 | dic[name] = numpy.array(value_list) |
|---|
| 1091 | setattr(self, varname, dic) |
|---|
| 1092 | |
|---|
| 1093 | def set_plot_state(self, figs, canvases): |
|---|
| 1094 | """ |
|---|
| 1095 | Build image state that wx.html understand |
|---|
| 1096 | by plotting, putting it into wx.FileSystem image object |
|---|
| 1097 | |
|---|
| 1098 | """ |
|---|
| 1099 | images = [] |
|---|
| 1100 | |
|---|
| 1101 | # Reset memory |
|---|
| 1102 | self.imgRAM = None |
|---|
| 1103 | wx.MemoryFSHandler() |
|---|
| 1104 | |
|---|
| 1105 | # For no figures in the list, prepare empty plot |
|---|
| 1106 | if figs is None or len(figs) == 0: |
|---|
| 1107 | figs = [None] |
|---|
| 1108 | |
|---|
| 1109 | # Loop over the list of figures |
|---|
| 1110 | # use wx.MemoryFSHandler |
|---|
| 1111 | self.imgRAM = wx.MemoryFSHandler() |
|---|
| 1112 | for fig in figs: |
|---|
| 1113 | if fig is not None: |
|---|
| 1114 | ind = figs.index(fig) |
|---|
| 1115 | canvas = canvases[ind] |
|---|
| 1116 | |
|---|
| 1117 | # store the image in wx.FileSystem Object |
|---|
| 1118 | wx.FileSystem.AddHandler(wx.MemoryFSHandler()) |
|---|
| 1119 | |
|---|
| 1120 | # index of the fig |
|---|
| 1121 | ind = figs.index(fig) |
|---|
| 1122 | |
|---|
| 1123 | # AddFile, image can be retrieved with 'memory:filename' |
|---|
| 1124 | self.imgRAM.AddFile('img_fit%s.png' % ind, |
|---|
| 1125 | canvas.bitmap, wx.BITMAP_TYPE_PNG) |
|---|
| 1126 | |
|---|
| 1127 | # append figs |
|---|
| 1128 | images.append(fig) |
|---|
| 1129 | |
|---|
| 1130 | return images |
|---|
| 1131 | |
|---|
| 1132 | |
|---|
| 1133 | class Reader(CansasReader): |
|---|
| 1134 | """ |
|---|
| 1135 | Class to load a .fitv fitting file |
|---|
| 1136 | """ |
|---|
| 1137 | # File type |
|---|
| 1138 | type_name = "Fitting" |
|---|
| 1139 | |
|---|
| 1140 | # Wildcards |
|---|
| 1141 | type = ["Fitting files (*.fitv)|*.fitv" |
|---|
| 1142 | "SASView file (*.svs)|*.svs"] |
|---|
| 1143 | # List of allowed extensions |
|---|
| 1144 | ext = ['.fitv', '.FITV', '.svs', 'SVS'] |
|---|
| 1145 | |
|---|
| 1146 | def __init__(self, call_back=None, cansas=True): |
|---|
| 1147 | CansasReader.__init__(self) |
|---|
| 1148 | """ |
|---|
| 1149 | Initialize the call-back method to be called |
|---|
| 1150 | after we load a file |
|---|
| 1151 | |
|---|
| 1152 | :param call_back: call-back method |
|---|
| 1153 | :param cansas: True = files will be written/read in CanSAS format |
|---|
| 1154 | False = write CanSAS format |
|---|
| 1155 | |
|---|
| 1156 | """ |
|---|
| 1157 | # Call back method to be executed after a file is read |
|---|
| 1158 | self.call_back = call_back |
|---|
| 1159 | # CanSAS format flag |
|---|
| 1160 | self.cansas = cansas |
|---|
| 1161 | self.state = None |
|---|
| 1162 | # batch fitting params for saving |
|---|
| 1163 | self.batchfit_params = [] |
|---|
| 1164 | |
|---|
| 1165 | def get_state(self): |
|---|
| 1166 | return self.state |
|---|
| 1167 | |
|---|
| 1168 | def read(self, path): |
|---|
| 1169 | """ |
|---|
| 1170 | Load a new P(r) inversion state from file |
|---|
| 1171 | |
|---|
| 1172 | :param path: file path |
|---|
| 1173 | |
|---|
| 1174 | """ |
|---|
| 1175 | if self.cansas: |
|---|
| 1176 | return self._read_cansas(path) |
|---|
| 1177 | |
|---|
| 1178 | def _data2d_to_xml_doc(self, datainfo): |
|---|
| 1179 | """ |
|---|
| 1180 | Create an XML document to contain the content of a Data2D |
|---|
| 1181 | |
|---|
| 1182 | :param datainfo: Data2D object |
|---|
| 1183 | |
|---|
| 1184 | """ |
|---|
| 1185 | if not issubclass(datainfo.__class__, Data2D): |
|---|
| 1186 | raise RuntimeError, "The cansas writer expects a Data2D instance" |
|---|
| 1187 | |
|---|
| 1188 | title = "cansas1d/%s" % self.version |
|---|
| 1189 | title += "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" |
|---|
| 1190 | doc = xml.dom.minidom.Document() |
|---|
| 1191 | main_node = doc.createElement("SASroot") |
|---|
| 1192 | main_node.setAttribute("version", self.version) |
|---|
| 1193 | main_node.setAttribute("xmlns", "cansas1d/%s" % self.version) |
|---|
| 1194 | main_node.setAttribute("xmlns:xsi", |
|---|
| 1195 | "http://www.w3.org/2001/XMLSchema-instance") |
|---|
| 1196 | main_node.setAttribute("xsi:schemaLocation", title) |
|---|
| 1197 | |
|---|
| 1198 | doc.appendChild(main_node) |
|---|
| 1199 | |
|---|
| 1200 | entry_node = doc.createElement("SASentry") |
|---|
| 1201 | main_node.appendChild(entry_node) |
|---|
| 1202 | |
|---|
| 1203 | write_node(doc, entry_node, "Title", datainfo.title) |
|---|
| 1204 | if datainfo is not None: |
|---|
| 1205 | write_node(doc, entry_node, "data_class", |
|---|
| 1206 | datainfo.__class__.__name__) |
|---|
| 1207 | for item in datainfo.run: |
|---|
| 1208 | runname = {} |
|---|
| 1209 | if item in datainfo.run_name and \ |
|---|
| 1210 | len(str(datainfo.run_name[item])) > 1: |
|---|
| 1211 | runname = {'name': datainfo.run_name[item]} |
|---|
| 1212 | write_node(doc, entry_node, "Run", item, runname) |
|---|
| 1213 | # Data info |
|---|
| 1214 | new_node = doc.createElement("SASdata") |
|---|
| 1215 | entry_node.appendChild(new_node) |
|---|
| 1216 | for item in LIST_OF_DATA_2D_ATTR: |
|---|
| 1217 | element = doc.createElement(item[0]) |
|---|
| 1218 | element.setAttribute(item[0], str(getattr(datainfo, item[1]))) |
|---|
| 1219 | new_node.appendChild(element) |
|---|
| 1220 | |
|---|
| 1221 | for item in LIST_OF_DATA_2D_VALUES: |
|---|
| 1222 | root_node = doc.createElement(item[0]) |
|---|
| 1223 | new_node.appendChild(root_node) |
|---|
| 1224 | temp_list = getattr(datainfo, item[1]) |
|---|
| 1225 | |
|---|
| 1226 | if temp_list is None or len(temp_list) == 0: |
|---|
| 1227 | element = doc.createElement(item[0]) |
|---|
| 1228 | element.appendChild(doc.createTextNode(str(temp_list))) |
|---|
| 1229 | root_node.appendChild(element) |
|---|
| 1230 | else: |
|---|
| 1231 | for value in temp_list: |
|---|
| 1232 | element = doc.createElement(item[0]) |
|---|
| 1233 | element.setAttribute(item[0], str(value)) |
|---|
| 1234 | root_node.appendChild(element) |
|---|
| 1235 | |
|---|
| 1236 | # Sample info |
|---|
| 1237 | sample = doc.createElement("SASsample") |
|---|
| 1238 | if datainfo.sample.name is not None: |
|---|
| 1239 | sample.setAttribute("name", str(datainfo.sample.name)) |
|---|
| 1240 | entry_node.appendChild(sample) |
|---|
| 1241 | write_node(doc, sample, "ID", str(datainfo.sample.ID)) |
|---|
| 1242 | write_node(doc, sample, "thickness", datainfo.sample.thickness, |
|---|
| 1243 | {"unit": datainfo.sample.thickness_unit}) |
|---|
| 1244 | write_node(doc, sample, "transmission", datainfo.sample.transmission) |
|---|
| 1245 | write_node(doc, sample, "temperature", datainfo.sample.temperature, |
|---|
| 1246 | {"unit": datainfo.sample.temperature_unit}) |
|---|
| 1247 | |
|---|
| 1248 | for item in datainfo.sample.details: |
|---|
| 1249 | write_node(doc, sample, "details", item) |
|---|
| 1250 | |
|---|
| 1251 | pos = doc.createElement("position") |
|---|
| 1252 | written = write_node(doc, pos, "x", datainfo.sample.position.x, |
|---|
| 1253 | {"unit": datainfo.sample.position_unit}) |
|---|
| 1254 | written = written | write_node(doc, pos, "y", |
|---|
| 1255 | datainfo.sample.position.y, |
|---|
| 1256 | {"unit": datainfo.sample.position_unit}) |
|---|
| 1257 | written = written | write_node(doc, pos, "z", |
|---|
| 1258 | datainfo.sample.position.z, |
|---|
| 1259 | {"unit": datainfo.sample.position_unit}) |
|---|
| 1260 | if written: |
|---|
| 1261 | sample.appendChild(pos) |
|---|
| 1262 | |
|---|
| 1263 | ori = doc.createElement("orientation") |
|---|
| 1264 | written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, |
|---|
| 1265 | {"unit": datainfo.sample.orientation_unit}) |
|---|
| 1266 | written = written | write_node(doc, ori, "pitch", |
|---|
| 1267 | datainfo.sample.orientation.y, |
|---|
| 1268 | {"unit": |
|---|
| 1269 | datainfo.sample.orientation_unit}) |
|---|
| 1270 | written = written | write_node(doc, ori, "yaw", |
|---|
| 1271 | datainfo.sample.orientation.z, |
|---|
| 1272 | {"unit": |
|---|
| 1273 | datainfo.sample.orientation_unit}) |
|---|
| 1274 | if written: |
|---|
| 1275 | sample.appendChild(ori) |
|---|
| 1276 | |
|---|
| 1277 | # Instrument info |
|---|
| 1278 | instr = doc.createElement("SASinstrument") |
|---|
| 1279 | entry_node.appendChild(instr) |
|---|
| 1280 | |
|---|
| 1281 | write_node(doc, instr, "name", datainfo.instrument) |
|---|
| 1282 | |
|---|
| 1283 | # Source |
|---|
| 1284 | source = doc.createElement("SASsource") |
|---|
| 1285 | if datainfo.source.name is not None: |
|---|
| 1286 | source.setAttribute("name", str(datainfo.source.name)) |
|---|
| 1287 | instr.appendChild(source) |
|---|
| 1288 | |
|---|
| 1289 | write_node(doc, source, "radiation", datainfo.source.radiation) |
|---|
| 1290 | write_node(doc, source, "beam_shape", datainfo.source.beam_shape) |
|---|
| 1291 | size = doc.createElement("beam_size") |
|---|
| 1292 | if datainfo.source.beam_size_name is not None: |
|---|
| 1293 | size.setAttribute("name", str(datainfo.source.beam_size_name)) |
|---|
| 1294 | written = write_node(doc, size, "x", datainfo.source.beam_size.x, |
|---|
| 1295 | {"unit": datainfo.source.beam_size_unit}) |
|---|
| 1296 | written = written | write_node(doc, size, "y", |
|---|
| 1297 | datainfo.source.beam_size.y, |
|---|
| 1298 | {"unit": datainfo.source.beam_size_unit}) |
|---|
| 1299 | written = written | write_node(doc, size, "z", |
|---|
| 1300 | datainfo.source.beam_size.z, |
|---|
| 1301 | {"unit": datainfo.source.beam_size_unit}) |
|---|
| 1302 | if written: |
|---|
| 1303 | source.appendChild(size) |
|---|
| 1304 | |
|---|
| 1305 | write_node(doc, source, "wavelength", datainfo.source.wavelength, |
|---|
| 1306 | {"unit": datainfo.source.wavelength_unit}) |
|---|
| 1307 | write_node(doc, source, "wavelength_min", |
|---|
| 1308 | datainfo.source.wavelength_min, |
|---|
| 1309 | {"unit": datainfo.source.wavelength_min_unit}) |
|---|
| 1310 | write_node(doc, source, "wavelength_max", |
|---|
| 1311 | datainfo.source.wavelength_max, |
|---|
| 1312 | {"unit": datainfo.source.wavelength_max_unit}) |
|---|
| 1313 | write_node(doc, source, "wavelength_spread", |
|---|
| 1314 | datainfo.source.wavelength_spread, |
|---|
| 1315 | {"unit": datainfo.source.wavelength_spread_unit}) |
|---|
| 1316 | |
|---|
| 1317 | # Collimation |
|---|
| 1318 | for item in datainfo.collimation: |
|---|
| 1319 | coll = doc.createElement("SAScollimation") |
|---|
| 1320 | if item.name is not None: |
|---|
| 1321 | coll.setAttribute("name", str(item.name)) |
|---|
| 1322 | instr.appendChild(coll) |
|---|
| 1323 | |
|---|
| 1324 | write_node(doc, coll, "length", item.length, |
|---|
| 1325 | {"unit": item.length_unit}) |
|---|
| 1326 | |
|---|
| 1327 | for apert in item.aperture: |
|---|
| 1328 | ap = doc.createElement("aperture") |
|---|
| 1329 | if apert.name is not None: |
|---|
| 1330 | ap.setAttribute("name", str(apert.name)) |
|---|
| 1331 | if apert.type is not None: |
|---|
| 1332 | ap.setAttribute("type", str(apert.type)) |
|---|
| 1333 | coll.appendChild(ap) |
|---|
| 1334 | |
|---|
| 1335 | write_node(doc, ap, "distance", apert.distance, |
|---|
| 1336 | {"unit": apert.distance_unit}) |
|---|
| 1337 | |
|---|
| 1338 | size = doc.createElement("size") |
|---|
| 1339 | if apert.size_name is not None: |
|---|
| 1340 | size.setAttribute("name", str(apert.size_name)) |
|---|
| 1341 | written = write_node(doc, size, "x", apert.size.x, |
|---|
| 1342 | {"unit": apert.size_unit}) |
|---|
| 1343 | written = written | write_node(doc, size, "y", apert.size.y, |
|---|
| 1344 | {"unit": apert.size_unit}) |
|---|
| 1345 | written = written | write_node(doc, size, "z", apert.size.z, |
|---|
| 1346 | {"unit": apert.size_unit}) |
|---|
| 1347 | if written: |
|---|
| 1348 | ap.appendChild(size) |
|---|
| 1349 | |
|---|
| 1350 | # Detectors |
|---|
| 1351 | for item in datainfo.detector: |
|---|
| 1352 | det = doc.createElement("SASdetector") |
|---|
| 1353 | written = write_node(doc, det, "name", item.name) |
|---|
| 1354 | written = written | write_node(doc, det, "SDD", item.distance, |
|---|
| 1355 | {"unit": item.distance_unit}) |
|---|
| 1356 | written = written | write_node(doc, det, "slit_length", |
|---|
| 1357 | item.slit_length, |
|---|
| 1358 | {"unit": item.slit_length_unit}) |
|---|
| 1359 | if written: |
|---|
| 1360 | instr.appendChild(det) |
|---|
| 1361 | |
|---|
| 1362 | off = doc.createElement("offset") |
|---|
| 1363 | written = write_node(doc, off, "x", item.offset.x, |
|---|
| 1364 | {"unit": item.offset_unit}) |
|---|
| 1365 | written = written | write_node(doc, off, "y", item.offset.y, |
|---|
| 1366 | {"unit": item.offset_unit}) |
|---|
| 1367 | written = written | write_node(doc, off, "z", item.offset.z, |
|---|
| 1368 | {"unit": item.offset_unit}) |
|---|
| 1369 | if written: |
|---|
| 1370 | det.appendChild(off) |
|---|
| 1371 | |
|---|
| 1372 | center = doc.createElement("beam_center") |
|---|
| 1373 | written = write_node(doc, center, "x", item.beam_center.x, |
|---|
| 1374 | {"unit": item.beam_center_unit}) |
|---|
| 1375 | written = written | write_node(doc, center, "y", |
|---|
| 1376 | item.beam_center.y, |
|---|
| 1377 | {"unit": item.beam_center_unit}) |
|---|
| 1378 | written = written | write_node(doc, center, "z", |
|---|
| 1379 | item.beam_center.z, |
|---|
| 1380 | {"unit": item.beam_center_unit}) |
|---|
| 1381 | if written: |
|---|
| 1382 | det.appendChild(center) |
|---|
| 1383 | |
|---|
| 1384 | pix = doc.createElement("pixel_size") |
|---|
| 1385 | written = write_node(doc, pix, "x", item.pixel_size.x, |
|---|
| 1386 | {"unit": item.pixel_size_unit}) |
|---|
| 1387 | written = written | write_node(doc, pix, "y", item.pixel_size.y, |
|---|
| 1388 | {"unit": item.pixel_size_unit}) |
|---|
| 1389 | written = written | write_node(doc, pix, "z", item.pixel_size.z, |
|---|
| 1390 | {"unit": item.pixel_size_unit}) |
|---|
| 1391 | if written: |
|---|
| 1392 | det.appendChild(pix) |
|---|
| 1393 | |
|---|
| 1394 | ori = doc.createElement("orientation") |
|---|
| 1395 | written = write_node(doc, ori, "roll", item.orientation.x, |
|---|
| 1396 | {"unit": item.orientation_unit}) |
|---|
| 1397 | written = written | write_node(doc, ori, "pitch", |
|---|
| 1398 | item.orientation.y, |
|---|
| 1399 | {"unit": item.orientation_unit}) |
|---|
| 1400 | written = written | write_node(doc, ori, "yaw", item.orientation.z, |
|---|
| 1401 | {"unit": item.orientation_unit}) |
|---|
| 1402 | if written: |
|---|
| 1403 | det.appendChild(ori) |
|---|
| 1404 | |
|---|
| 1405 | # Processes info |
|---|
| 1406 | for item in datainfo.process: |
|---|
| 1407 | node = doc.createElement("SASprocess") |
|---|
| 1408 | entry_node.appendChild(node) |
|---|
| 1409 | |
|---|
| 1410 | write_node(doc, node, "name", item.name) |
|---|
| 1411 | write_node(doc, node, "date", item.date) |
|---|
| 1412 | write_node(doc, node, "description", item.description) |
|---|
| 1413 | for term in item.term: |
|---|
| 1414 | value = term['value'] |
|---|
| 1415 | del term['value'] |
|---|
| 1416 | write_node(doc, node, "term", value, term) |
|---|
| 1417 | for note in item.notes: |
|---|
| 1418 | write_node(doc, node, "SASprocessnote", note) |
|---|
| 1419 | # Return the document, and the SASentry node associated with |
|---|
| 1420 | # the data we just wrote |
|---|
| 1421 | return doc, entry_node |
|---|
| 1422 | |
|---|
| 1423 | def _parse_state(self, entry): |
|---|
| 1424 | """ |
|---|
| 1425 | Read a fit result from an XML node |
|---|
| 1426 | |
|---|
| 1427 | :param entry: XML node to read from |
|---|
| 1428 | :return: PageState object |
|---|
| 1429 | """ |
|---|
| 1430 | # Create an empty state |
|---|
| 1431 | state = None |
|---|
| 1432 | # Locate the P(r) node |
|---|
| 1433 | try: |
|---|
| 1434 | nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, |
|---|
| 1435 | namespaces={'ns': CANSAS_NS}) |
|---|
| 1436 | if nodes: |
|---|
| 1437 | # Create an empty state |
|---|
| 1438 | state = PageState() |
|---|
| 1439 | state.from_xml(node=nodes[0]) |
|---|
| 1440 | |
|---|
| 1441 | except: |
|---|
| 1442 | logging.info("XML document does not contain fitting information.\n" |
|---|
| 1443 | + traceback.format_exc()) |
|---|
| 1444 | |
|---|
| 1445 | return state |
|---|
| 1446 | |
|---|
| 1447 | def _parse_simfit_state(self, entry): |
|---|
| 1448 | """ |
|---|
| 1449 | Parses the saved data for a simultaneous fit |
|---|
| 1450 | :param entry: XML object to read from |
|---|
| 1451 | :return: XML object for a simultaneous fit or None |
|---|
| 1452 | """ |
|---|
| 1453 | nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, |
|---|
| 1454 | namespaces={'ns': CANSAS_NS}) |
|---|
| 1455 | if nodes: |
|---|
| 1456 | simfitstate = nodes[0].xpath('ns:simultaneous_fit', |
|---|
| 1457 | namespaces={'ns': CANSAS_NS}) |
|---|
| 1458 | if simfitstate: |
|---|
| 1459 | from simfitpage import SimFitPageState |
|---|
| 1460 | sim_fit_state = SimFitPageState() |
|---|
| 1461 | simfitstate_0 = simfitstate[0] |
|---|
| 1462 | all = simfitstate_0.xpath('ns:select_all', |
|---|
| 1463 | namespaces={'ns': CANSAS_NS}) |
|---|
| 1464 | atts = all[0].attrib |
|---|
| 1465 | checked = atts.get('checked') |
|---|
| 1466 | sim_fit_state.select_all = bool(checked) |
|---|
| 1467 | model_list = simfitstate_0.xpath('ns:model_list', |
|---|
| 1468 | namespaces={'ns': CANSAS_NS}) |
|---|
| 1469 | model_list_items = model_list[0].xpath('ns:model_list_item', |
|---|
| 1470 | namespaces={'ns': |
|---|
| 1471 | CANSAS_NS}) |
|---|
| 1472 | for model in model_list_items: |
|---|
| 1473 | attrs = model.attrib |
|---|
| 1474 | sim_fit_state.model_list.append(attrs) |
|---|
| 1475 | |
|---|
| 1476 | constraints = simfitstate_0.xpath('ns:constraints', |
|---|
| 1477 | namespaces={'ns': CANSAS_NS}) |
|---|
| 1478 | constraint_list = constraints[0].xpath('ns:constraint', |
|---|
| 1479 | namespaces={'ns': CANSAS_NS}) |
|---|
| 1480 | for constraint in constraint_list: |
|---|
| 1481 | attrs = constraint.attrib |
|---|
| 1482 | sim_fit_state.constraints_list.append(attrs) |
|---|
| 1483 | |
|---|
| 1484 | return sim_fit_state |
|---|
| 1485 | else: |
|---|
| 1486 | return None |
|---|
| 1487 | |
|---|
| 1488 | def _parse_save_state_entry(self, dom): |
|---|
| 1489 | """ |
|---|
| 1490 | Parse a SASentry |
|---|
| 1491 | |
|---|
| 1492 | :param node: SASentry node |
|---|
| 1493 | |
|---|
| 1494 | :return: Data1D/Data2D object |
|---|
| 1495 | |
|---|
| 1496 | """ |
|---|
| 1497 | node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS}) |
|---|
| 1498 | if not node or node[0].text.lstrip().rstrip() != "Data2D": |
|---|
| 1499 | return_value, _ = self._parse_entry(dom) |
|---|
| 1500 | numpy.trim_zeros(return_value.x) |
|---|
| 1501 | numpy.trim_zeros(return_value.y) |
|---|
| 1502 | numpy.trim_zeros(return_value.dy) |
|---|
| 1503 | size_dx = return_value.dx.size |
|---|
| 1504 | size_dxl = return_value.dxl.size |
|---|
| 1505 | size_dxw = return_value.dxw.size |
|---|
| 1506 | if size_dxl == 0 and size_dxw == 0: |
|---|
| 1507 | return_value.dxl = None |
|---|
| 1508 | return_value.dxw = None |
|---|
| 1509 | numpy.trim_zeros(return_value.dx) |
|---|
| 1510 | elif size_dx == 0: |
|---|
| 1511 | return_value.dx = None |
|---|
| 1512 | size_dx = size_dxl |
|---|
| 1513 | numpy.trim_zeros(return_value.dxl) |
|---|
| 1514 | numpy.trim_zeros(return_value.dxw) |
|---|
| 1515 | |
|---|
| 1516 | return return_value, _ |
|---|
| 1517 | |
|---|
| 1518 | # Parse 2D |
|---|
| 1519 | data_info = Data2D() |
|---|
| 1520 | |
|---|
| 1521 | # Look up title |
|---|
| 1522 | self._store_content('ns:Title', dom, 'title', data_info) |
|---|
| 1523 | |
|---|
| 1524 | # Look up run number |
|---|
| 1525 | nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS}) |
|---|
| 1526 | for item in nodes: |
|---|
| 1527 | if item.text is not None: |
|---|
| 1528 | value = item.text.strip() |
|---|
| 1529 | if len(value) > 0: |
|---|
| 1530 | data_info.run.append(value) |
|---|
| 1531 | if item.get('name') is not None: |
|---|
| 1532 | data_info.run_name[value] = item.get('name') |
|---|
| 1533 | |
|---|
| 1534 | # Look up instrument name |
|---|
| 1535 | self._store_content('ns:SASinstrument/ns:name', dom, |
|---|
| 1536 | 'instrument', data_info) |
|---|
| 1537 | |
|---|
| 1538 | # Notes |
|---|
| 1539 | note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS}) |
|---|
| 1540 | for note in note_list: |
|---|
| 1541 | try: |
|---|
| 1542 | if note.text is not None: |
|---|
| 1543 | note_value = note.text.strip() |
|---|
| 1544 | if len(note_value) > 0: |
|---|
| 1545 | data_info.notes.append(note_value) |
|---|
| 1546 | except Exception: |
|---|
| 1547 | err_mess = "cansas_reader.read: error processing entry notes\n" |
|---|
| 1548 | err_mess += " %s" % sys.exc_value |
|---|
| 1549 | self.errors.append(err_mess) |
|---|
| 1550 | logging.error(err_mess) |
|---|
| 1551 | |
|---|
| 1552 | # Sample info ################### |
|---|
| 1553 | entry = get_content('ns:SASsample', dom) |
|---|
| 1554 | if entry is not None: |
|---|
| 1555 | data_info.sample.name = entry.get('name') |
|---|
| 1556 | |
|---|
| 1557 | self._store_content('ns:SASsample/ns:ID', dom, 'ID', data_info.sample) |
|---|
| 1558 | self._store_float('ns:SASsample/ns:thickness', dom, 'thickness', |
|---|
| 1559 | data_info.sample) |
|---|
| 1560 | self._store_float('ns:SASsample/ns:transmission', dom, 'transmission', |
|---|
| 1561 | data_info.sample) |
|---|
| 1562 | self._store_float('ns:SASsample/ns:temperature', dom, 'temperature', |
|---|
| 1563 | data_info.sample) |
|---|
| 1564 | |
|---|
| 1565 | nodes = dom.xpath('ns:SASsample/ns:details', |
|---|
| 1566 | namespaces={'ns': CANSAS_NS}) |
|---|
| 1567 | for item in nodes: |
|---|
| 1568 | try: |
|---|
| 1569 | if item.text is not None: |
|---|
| 1570 | detail_value = item.text.strip() |
|---|
| 1571 | if len(detail_value) > 0: |
|---|
| 1572 | data_info.sample.details.append(detail_value) |
|---|
| 1573 | except Exception: |
|---|
| 1574 | err_mess = "cansas_reader.read: error processing entry notes\n" |
|---|
| 1575 | err_mess += " %s" % sys.exc_value |
|---|
| 1576 | self.errors.append(err_mess) |
|---|
| 1577 | logging.error(err_mess) |
|---|
| 1578 | |
|---|
| 1579 | # Position (as a vector) |
|---|
| 1580 | self._store_float('ns:SASsample/ns:position/ns:x', dom, 'position.x', |
|---|
| 1581 | data_info.sample) |
|---|
| 1582 | self._store_float('ns:SASsample/ns:position/ns:y', dom, 'position.y', |
|---|
| 1583 | data_info.sample) |
|---|
| 1584 | self._store_float('ns:SASsample/ns:position/ns:z', dom, 'position.z', |
|---|
| 1585 | data_info.sample) |
|---|
| 1586 | |
|---|
| 1587 | # Orientation (as a vector) |
|---|
| 1588 | self._store_float('ns:SASsample/ns:orientation/ns:roll', |
|---|
| 1589 | dom, 'orientation.x', data_info.sample) |
|---|
| 1590 | self._store_float('ns:SASsample/ns:orientation/ns:pitch', |
|---|
| 1591 | dom, 'orientation.y', data_info.sample) |
|---|
| 1592 | self._store_float('ns:SASsample/ns:orientation/ns:yaw', |
|---|
| 1593 | dom, 'orientation.z', data_info.sample) |
|---|
| 1594 | |
|---|
| 1595 | # Source info ################### |
|---|
| 1596 | entry = get_content('ns:SASinstrument/ns:SASsource', dom) |
|---|
| 1597 | if entry is not None: |
|---|
| 1598 | data_info.source.name = entry.get('name') |
|---|
| 1599 | |
|---|
| 1600 | self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation', |
|---|
| 1601 | dom, 'radiation', data_info.source) |
|---|
| 1602 | self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape', |
|---|
| 1603 | dom, 'beam_shape', data_info.source) |
|---|
| 1604 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength', |
|---|
| 1605 | dom, 'wavelength', data_info.source) |
|---|
| 1606 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min', |
|---|
| 1607 | dom, 'wavelength_min', data_info.source) |
|---|
| 1608 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max', |
|---|
| 1609 | dom, 'wavelength_max', data_info.source) |
|---|
| 1610 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread', |
|---|
| 1611 | dom, 'wavelength_spread', data_info.source) |
|---|
| 1612 | |
|---|
| 1613 | # Beam size (as a vector) |
|---|
| 1614 | entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom) |
|---|
| 1615 | if entry is not None: |
|---|
| 1616 | data_info.source.beam_size_name = entry.get('name') |
|---|
| 1617 | |
|---|
| 1618 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x', |
|---|
| 1619 | dom, 'beam_size.x', data_info.source) |
|---|
| 1620 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y', |
|---|
| 1621 | dom, 'beam_size.y', data_info.source) |
|---|
| 1622 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z', |
|---|
| 1623 | dom, 'beam_size.z', data_info.source) |
|---|
| 1624 | |
|---|
| 1625 | # Collimation info ################### |
|---|
| 1626 | nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', |
|---|
| 1627 | namespaces={'ns': CANSAS_NS}) |
|---|
| 1628 | for item in nodes: |
|---|
| 1629 | collim = Collimation() |
|---|
| 1630 | if item.get('name') is not None: |
|---|
| 1631 | collim.name = item.get('name') |
|---|
| 1632 | self._store_float('ns:length', item, 'length', collim) |
|---|
| 1633 | |
|---|
| 1634 | # Look for apertures |
|---|
| 1635 | apert_list = item.xpath('ns:aperture', |
|---|
| 1636 | namespaces={'ns': CANSAS_NS}) |
|---|
| 1637 | for apert in apert_list: |
|---|
| 1638 | aperture = Aperture() |
|---|
| 1639 | |
|---|
| 1640 | # Get the name and type of the aperture |
|---|
| 1641 | aperture.name = apert.get('name') |
|---|
| 1642 | aperture.type = apert.get('type') |
|---|
| 1643 | |
|---|
| 1644 | self._store_float('ns:distance', apert, 'distance', aperture) |
|---|
| 1645 | |
|---|
| 1646 | entry = get_content('ns:size', apert) |
|---|
| 1647 | if entry is not None: |
|---|
| 1648 | aperture.size_name = entry.get('name') |
|---|
| 1649 | |
|---|
| 1650 | self._store_float('ns:size/ns:x', apert, 'size.x', aperture) |
|---|
| 1651 | self._store_float('ns:size/ns:y', apert, 'size.y', aperture) |
|---|
| 1652 | self._store_float('ns:size/ns:z', apert, 'size.z', aperture) |
|---|
| 1653 | |
|---|
| 1654 | collim.aperture.append(aperture) |
|---|
| 1655 | |
|---|
| 1656 | data_info.collimation.append(collim) |
|---|
| 1657 | |
|---|
| 1658 | # Detector info ###################### |
|---|
| 1659 | nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', |
|---|
| 1660 | namespaces={'ns': CANSAS_NS}) |
|---|
| 1661 | for item in nodes: |
|---|
| 1662 | |
|---|
| 1663 | detector = Detector() |
|---|
| 1664 | |
|---|
| 1665 | self._store_content('ns:name', item, 'name', detector) |
|---|
| 1666 | self._store_float('ns:SDD', item, 'distance', detector) |
|---|
| 1667 | |
|---|
| 1668 | # Detector offset (as a vector) |
|---|
| 1669 | self._store_float('ns:offset/ns:x', item, 'offset.x', detector) |
|---|
| 1670 | self._store_float('ns:offset/ns:y', item, 'offset.y', detector) |
|---|
| 1671 | self._store_float('ns:offset/ns:z', item, 'offset.z', detector) |
|---|
| 1672 | |
|---|
| 1673 | # Detector orientation (as a vector) |
|---|
| 1674 | self._store_float('ns:orientation/ns:roll', item, |
|---|
| 1675 | 'orientation.x', detector) |
|---|
| 1676 | self._store_float('ns:orientation/ns:pitch', item, |
|---|
| 1677 | 'orientation.y', detector) |
|---|
| 1678 | self._store_float('ns:orientation/ns:yaw', item, |
|---|
| 1679 | 'orientation.z', detector) |
|---|
| 1680 | |
|---|
| 1681 | # Beam center (as a vector) |
|---|
| 1682 | self._store_float('ns:beam_center/ns:x', item, |
|---|
| 1683 | 'beam_center.x', detector) |
|---|
| 1684 | self._store_float('ns:beam_center/ns:y', item, |
|---|
| 1685 | 'beam_center.y', detector) |
|---|
| 1686 | self._store_float('ns:beam_center/ns:z', item, |
|---|
| 1687 | 'beam_center.z', detector) |
|---|
| 1688 | |
|---|
| 1689 | # Pixel size (as a vector) |
|---|
| 1690 | self._store_float('ns:pixel_size/ns:x', item, |
|---|
| 1691 | 'pixel_size.x', detector) |
|---|
| 1692 | self._store_float('ns:pixel_size/ns:y', item, |
|---|
| 1693 | 'pixel_size.y', detector) |
|---|
| 1694 | self._store_float('ns:pixel_size/ns:z', item, |
|---|
| 1695 | 'pixel_size.z', detector) |
|---|
| 1696 | |
|---|
| 1697 | self._store_float('ns:slit_length', item, 'slit_length', detector) |
|---|
| 1698 | |
|---|
| 1699 | data_info.detector.append(detector) |
|---|
| 1700 | |
|---|
| 1701 | # Processes info ###################### |
|---|
| 1702 | nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS}) |
|---|
| 1703 | for item in nodes: |
|---|
| 1704 | process = Process() |
|---|
| 1705 | self._store_content('ns:name', item, 'name', process) |
|---|
| 1706 | self._store_content('ns:date', item, 'date', process) |
|---|
| 1707 | self._store_content('ns:description', item, 'description', process) |
|---|
| 1708 | |
|---|
| 1709 | term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS}) |
|---|
| 1710 | for term in term_list: |
|---|
| 1711 | try: |
|---|
| 1712 | term_attr = {} |
|---|
| 1713 | for attr in term.keys(): |
|---|
| 1714 | term_attr[attr] = term.get(attr).strip() |
|---|
| 1715 | if term.text is not None: |
|---|
| 1716 | term_attr['value'] = term.text.strip() |
|---|
| 1717 | process.term.append(term_attr) |
|---|
| 1718 | except: |
|---|
| 1719 | err_mess = "cansas_reader.read: error processing " |
|---|
| 1720 | err_mess += "entry notes\n %s" % sys.exc_value |
|---|
| 1721 | self.errors.append(err_mess) |
|---|
| 1722 | logging.error(err_mess) |
|---|
| 1723 | |
|---|
| 1724 | note_list = item.xpath('ns:SASprocessnote', |
|---|
| 1725 | namespaces={'ns': CANSAS_NS}) |
|---|
| 1726 | for note in note_list: |
|---|
| 1727 | if note.text is not None: |
|---|
| 1728 | process.notes.append(note.text.strip()) |
|---|
| 1729 | |
|---|
| 1730 | data_info.process.append(process) |
|---|
| 1731 | |
|---|
| 1732 | # Data info ###################### |
|---|
| 1733 | nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS}) |
|---|
| 1734 | if len(nodes) > 1: |
|---|
| 1735 | raise RuntimeError, "CanSAS reader is not compatible with" + \ |
|---|
| 1736 | " multiple SASdata entries" |
|---|
| 1737 | |
|---|
| 1738 | for entry in nodes: |
|---|
| 1739 | for item in LIST_OF_DATA_2D_ATTR: |
|---|
| 1740 | # get node |
|---|
| 1741 | node = get_content('ns:%s' % item[0], entry) |
|---|
| 1742 | setattr(data_info, item[1], parse_entry_helper(node, item)) |
|---|
| 1743 | |
|---|
| 1744 | for item in LIST_OF_DATA_2D_VALUES: |
|---|
| 1745 | field = get_content('ns:%s' % item[0], entry) |
|---|
| 1746 | value_list = [] |
|---|
| 1747 | if field is not None: |
|---|
| 1748 | value_list = \ |
|---|
| 1749 | [parse_entry_helper(node, item) for node in field] |
|---|
| 1750 | if len(value_list) < 2: |
|---|
| 1751 | setattr(data_info, item[0], None) |
|---|
| 1752 | else: |
|---|
| 1753 | setattr(data_info, item[0], numpy.array(value_list)) |
|---|
| 1754 | |
|---|
| 1755 | return data_info |
|---|
| 1756 | |
|---|
| 1757 | def _read_cansas(self, path): |
|---|
| 1758 | """ |
|---|
| 1759 | Load data and fitting information from a CanSAS XML file. |
|---|
| 1760 | |
|---|
| 1761 | :param path: file path |
|---|
| 1762 | :return: Data1D object if a single SASentry was found, |
|---|
| 1763 | or a list of Data1D objects if multiple entries were found, |
|---|
| 1764 | or None of nothing was found |
|---|
| 1765 | :raise RuntimeError: when the file can't be opened |
|---|
| 1766 | :raise ValueError: when the length of the data vectors are inconsistent |
|---|
| 1767 | """ |
|---|
| 1768 | output = [] |
|---|
| 1769 | simfitstate = None |
|---|
| 1770 | basename = os.path.basename(path) |
|---|
| 1771 | root, extension = os.path.splitext(basename) |
|---|
| 1772 | ext = extension.lower() |
|---|
| 1773 | try: |
|---|
| 1774 | if os.path.isfile(path): |
|---|
| 1775 | if ext in self.ext or ext == '.xml': |
|---|
| 1776 | tree = etree.parse(path, parser=etree.ETCompatXMLParser()) |
|---|
| 1777 | # Check the format version number |
|---|
| 1778 | # Specifying the namespace will take care of the file |
|---|
| 1779 | # format version |
|---|
| 1780 | root = tree.getroot() |
|---|
| 1781 | entry_list = root.xpath('ns:SASentry', |
|---|
| 1782 | namespaces={'ns': CANSAS_NS}) |
|---|
| 1783 | for entry in entry_list: |
|---|
| 1784 | try: |
|---|
| 1785 | sas_entry, _ = self._parse_save_state_entry(entry) |
|---|
| 1786 | except: |
|---|
| 1787 | raise |
|---|
| 1788 | fitstate = self._parse_state(entry) |
|---|
| 1789 | |
|---|
| 1790 | # state could be None when .svs file is loaded |
|---|
| 1791 | # in this case, skip appending to output |
|---|
| 1792 | if fitstate is not None: |
|---|
| 1793 | sas_entry.meta_data['fitstate'] = fitstate |
|---|
| 1794 | sas_entry.filename = fitstate.file |
|---|
| 1795 | output.append(sas_entry) |
|---|
| 1796 | |
|---|
| 1797 | else: |
|---|
| 1798 | self.call_back(format=ext) |
|---|
| 1799 | raise RuntimeError, "%s is not a file" % path |
|---|
| 1800 | |
|---|
| 1801 | # Return output consistent with the loader's api |
|---|
| 1802 | if len(output) == 0: |
|---|
| 1803 | self.call_back(state=None, datainfo=None, format=ext) |
|---|
| 1804 | return None |
|---|
| 1805 | else: |
|---|
| 1806 | for ind in range(len(output)): |
|---|
| 1807 | # Call back to post the new state |
|---|
| 1808 | state = output[ind].meta_data['fitstate'] |
|---|
| 1809 | t = time.localtime(state.timestamp) |
|---|
| 1810 | time_str = time.strftime("%b %d %H:%M", t) |
|---|
| 1811 | # Check that no time stamp is already appended |
|---|
| 1812 | max_char = state.file.find("[") |
|---|
| 1813 | if max_char < 0: |
|---|
| 1814 | max_char = len(state.file) |
|---|
| 1815 | original_fname = state.file[0:max_char] |
|---|
| 1816 | state.file = original_fname + ' [' + time_str + ']' |
|---|
| 1817 | |
|---|
| 1818 | if state is not None and state.is_data is not None: |
|---|
| 1819 | output[ind].is_data = state.is_data |
|---|
| 1820 | |
|---|
| 1821 | output[ind].filename = state.file |
|---|
| 1822 | state.data = output[ind] |
|---|
| 1823 | state.data.name = output[ind].filename # state.data_name |
|---|
| 1824 | state.data.id = state.data_id |
|---|
| 1825 | if state.is_data is not None: |
|---|
| 1826 | state.data.is_data = state.is_data |
|---|
| 1827 | if output[ind].run_name is not None\ |
|---|
| 1828 | and len(output[ind].run_name) != 0: |
|---|
| 1829 | if isinstance(output[ind].run_name, dict): |
|---|
| 1830 | name = output[ind].run_name.keys()[0] |
|---|
| 1831 | else: |
|---|
| 1832 | name = output[ind].run_name |
|---|
| 1833 | else: |
|---|
| 1834 | name = original_fname |
|---|
| 1835 | state.data.group_id = name |
|---|
| 1836 | # store state in fitting |
|---|
| 1837 | self.call_back(state=state, |
|---|
| 1838 | datainfo=output[ind], format=ext) |
|---|
| 1839 | self.state = state |
|---|
| 1840 | simfitstate = self._parse_simfit_state(entry) |
|---|
| 1841 | if simfitstate is not None: |
|---|
| 1842 | self.call_back(state=simfitstate) |
|---|
| 1843 | |
|---|
| 1844 | return output |
|---|
| 1845 | except: |
|---|
| 1846 | self.call_back(format=ext) |
|---|
| 1847 | raise |
|---|
| 1848 | |
|---|
| 1849 | def write(self, filename, datainfo=None, fitstate=None): |
|---|
| 1850 | """ |
|---|
| 1851 | Write the content of a Data1D as a CanSAS XML file only for standalone |
|---|
| 1852 | |
|---|
| 1853 | :param filename: name of the file to write |
|---|
| 1854 | :param datainfo: Data1D object |
|---|
| 1855 | :param fitstate: PageState object |
|---|
| 1856 | |
|---|
| 1857 | """ |
|---|
| 1858 | # Sanity check |
|---|
| 1859 | if self.cansas: |
|---|
| 1860 | # Add fitting information to the XML document |
|---|
| 1861 | doc = self.write_toXML(datainfo, fitstate) |
|---|
| 1862 | # Write the XML document |
|---|
| 1863 | else: |
|---|
| 1864 | doc = fitstate.to_xml(file=filename) |
|---|
| 1865 | |
|---|
| 1866 | # Save the document no matter the type |
|---|
| 1867 | fd = open(filename, 'w') |
|---|
| 1868 | fd.write(doc.toprettyxml()) |
|---|
| 1869 | fd.close() |
|---|
| 1870 | |
|---|
| 1871 | def write_toXML(self, datainfo=None, state=None, batchfit=None): |
|---|
| 1872 | """ |
|---|
| 1873 | Write toXML, a helper for write(), |
|---|
| 1874 | could be used by guimanager._on_save() |
|---|
| 1875 | |
|---|
| 1876 | : return: xml doc |
|---|
| 1877 | """ |
|---|
| 1878 | |
|---|
| 1879 | self.batchfit_params = batchfit |
|---|
| 1880 | if state.data is None or not state.data.is_data: |
|---|
| 1881 | return None |
|---|
| 1882 | # make sure title and data run are filled. |
|---|
| 1883 | if state.data.title is None or state.data.title == '': |
|---|
| 1884 | state.data.title = state.data.name |
|---|
| 1885 | if state.data.run_name is None or state.data.run_name == {}: |
|---|
| 1886 | state.data.run = [str(state.data.name)] |
|---|
| 1887 | state.data.run_name[0] = state.data.name |
|---|
| 1888 | |
|---|
| 1889 | if issubclass(state.data.__class__, |
|---|
| 1890 | sas.sascalc.dataloader.data_info.Data1D): |
|---|
| 1891 | data = state.data |
|---|
| 1892 | doc, sasentry = self._to_xml_doc(data) |
|---|
| 1893 | else: |
|---|
| 1894 | data = state.data |
|---|
| 1895 | doc, sasentry = self._data2d_to_xml_doc(data) |
|---|
| 1896 | |
|---|
| 1897 | if state is not None: |
|---|
| 1898 | doc = state.to_xml(doc=doc, file=data.filename, entry_node=sasentry, |
|---|
| 1899 | batch_fit_state=self.batchfit_params) |
|---|
| 1900 | |
|---|
| 1901 | return doc |
|---|
| 1902 | |
|---|
| 1903 | # Simple html report templet |
|---|
| 1904 | HEADER = "<html>\n" |
|---|
| 1905 | HEADER += "<head>\n" |
|---|
| 1906 | HEADER += "<meta http-equiv=Content-Type content='text/html; " |
|---|
| 1907 | HEADER += "charset=windows-1252'> \n" |
|---|
| 1908 | HEADER += "<meta name=Generator >\n" |
|---|
| 1909 | HEADER += "</head>\n" |
|---|
| 1910 | HEADER += "<body lang=EN-US>\n" |
|---|
| 1911 | HEADER += "<div class=WordSection1>\n" |
|---|
| 1912 | HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >" |
|---|
| 1913 | HEADER += "%s</font></center></span></center></b></p>" |
|---|
| 1914 | HEADER += "<p class=MsoNormal> </p>" |
|---|
| 1915 | PARA = "<p class=MsoNormal><font size='4' > %s \n" |
|---|
| 1916 | PARA += "</font></p>" |
|---|
| 1917 | CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n" |
|---|
| 1918 | CENTRE += "</font></center></p>" |
|---|
| 1919 | FEET_1 = \ |
|---|
| 1920 | """ |
|---|
| 1921 | <p class=MsoNormal> </p> |
|---|
| 1922 | <br> |
|---|
| 1923 | <p class=MsoNormal><b><span ><center> <font size='4' > Graph |
|---|
| 1924 | </font></span></center></b></p> |
|---|
| 1925 | <p class=MsoNormal> </p> |
|---|
| 1926 | <center> |
|---|
| 1927 | <br><font size='4' >Model Computation</font> |
|---|
| 1928 | <br><font size='4' >Data: "%s"</font><br> |
|---|
| 1929 | """ |
|---|
| 1930 | FEET_2 = \ |
|---|
| 1931 | """ |
|---|
| 1932 | <img src="%s" > |
|---|
| 1933 | </img> |
|---|
| 1934 | """ |
|---|
| 1935 | FEET_3 = \ |
|---|
| 1936 | """ |
|---|
| 1937 | </center> |
|---|
| 1938 | </div> |
|---|
| 1939 | </body> |
|---|
| 1940 | </html> |
|---|
| 1941 | """ |
|---|
| 1942 | ELINE = "<p class=MsoNormal> </p>" |
|---|
