[f32d144] | 1 | """ |
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| 2 | Class that holds a fit page state |
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| 3 | """ |
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[a95ae9a] | 4 | # TODO: Refactor code so we don't need to use getattr/setattr |
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[5062bbf] | 5 | ################################################################################ |
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[a95ae9a] | 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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[5062bbf] | 9 | # |
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[a95ae9a] | 10 | # See the license text in license.txt |
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[5062bbf] | 11 | # |
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[a95ae9a] | 12 | # copyright 2009, University of Tennessee |
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[5062bbf] | 13 | ################################################################################ |
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[11a7e11] | 14 | import time |
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| 15 | import os |
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| 16 | import sys |
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[abcbe09] | 17 | import wx |
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[6f023e8] | 18 | import copy |
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[11a7e11] | 19 | import logging |
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[df7ed14] | 20 | import numpy |
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[7673ecd] | 21 | import traceback |
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[c77d859] | 22 | |
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[35b556d] | 23 | import xml.dom.minidom |
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[ac5b69d] | 24 | from xml.dom.minidom import parseString |
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[11a7e11] | 25 | from lxml import etree |
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| 26 | |
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[8898558b] | 27 | from sasmodels import convert |
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[6c382da] | 28 | import sasmodels.weights |
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| 29 | |
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[b699768] | 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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[a95ae9a] | 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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[61cada5] | 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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[b1e609c] | 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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[acf8e4a5] | 45 | LIST_OF_STATE_ATTRIBUTES = [["qmin", "qmin", "float"], |
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[b1e609c] | 46 | ["qmax", "qmax", "float"], |
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| 47 | ["npts", "npts", "float"], |
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| 48 | ["categorycombobox", "categorycombobox", "string"], |
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[c8e1996] | 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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[b1e609c] | 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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[c8e1996] | 70 | ["dq_l", "dq_l", "float"], |
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| 71 | ["dq_r", "dq_r", "float"], |
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[b1e609c] | 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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[11a7e11] | 78 | ["weights", "weights"]] |
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| 79 | |
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[b1e609c] | 80 | DISPERSION_LIST = [["disp_obj_dict", "_disp_obj_dict", "string"]] |
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[2296316] | 81 | |
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[b1e609c] | 82 | LIST_OF_STATE_PARAMETERS = [["parameters", "parameters"], |
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[f32d144] | 83 | ["str_parameters", "str_parameters"], |
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[61cada5] | 84 | ["orientation_parameters", "orientation_params"], |
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[c8e1996] | 85 | ["dispersity_parameters", |
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| 86 | "orientation_params_disp"], |
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[f32d144] | 87 | ["fixed_param", "fixed_param"], |
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| 88 | ["fittable_param", "fittable_param"]] |
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[b1e609c] | 89 | LIST_OF_DATA_2D_ATTR = [["xmin", "xmin", "float"], |
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[f32d144] | 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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[df7ed14] | 94 | ["_xunit", "_xunit", "string"], |
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[f32d144] | 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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[b1e609c] | 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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[61cada5] | 107 | |
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[f32d144] | 108 | |
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| 109 | def parse_entry_helper(node, item): |
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[0b12abb5] | 110 | """ |
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| 111 | Create a numpy list from value extrated from the node |
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[2f4b430] | 112 | |
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[0b12abb5] | 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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[f32d144] | 115 | attribute and the third one is the type of the value of that |
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[0b12abb5] | 116 | attribute. type can be string, float, bool, etc. |
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[2f4b430] | 117 | |
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[0b12abb5] | 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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[e3d1423] | 125 | return node.get(item[0]).strip() == "True" |
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[c8e1996] | 126 | except Exception: |
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[0b12abb5] | 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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[c8e1996] | 131 | except Exception: |
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[0b12abb5] | 132 | return None |
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[2f4b430] | 133 | |
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| 134 | |
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[cfc0913] | 135 | class PageState(object): |
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[c77d859] | 136 | """ |
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[5062bbf] | 137 | Contains information to reconstruct a page of the fitpanel. |
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[c77d859] | 138 | """ |
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[61cada5] | 139 | def __init__(self, parent=None, model=None, data=None): |
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[f32d144] | 140 | """ |
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[5062bbf] | 141 | Initialize the current state |
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[2f4b430] | 142 | |
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[5062bbf] | 143 | :param model: a selected model within a page |
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[f32d144] | 144 | :param data: |
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[2f4b430] | 145 | |
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[c77d859] | 146 | """ |
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[61cada5] | 147 | self.file = None |
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[a95ae9a] | 148 | # Time of state creation |
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[11a7e11] | 149 | self.timestamp = time.time() |
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[a95ae9a] | 150 | # Data member to store the dispersion object created |
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[c77d859] | 151 | self._disp_obj_dict = {} |
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[a95ae9a] | 152 | # ------------------------ |
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| 153 | # Data used for fitting |
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[c77d859] | 154 | self.data = data |
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[2296316] | 155 | # model data |
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| 156 | self.theory_data = None |
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[a95ae9a] | 157 | # Is 2D |
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[2296316] | 158 | self.is_2D = False |
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| 159 | self.images = None |
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[2f4b430] | 160 | |
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[a95ae9a] | 161 | # save additional information on data that dataloader.reader |
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| 162 | # does not read |
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[61cada5] | 163 | self.is_data = None |
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| 164 | self.data_name = "" |
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[c0ff8cc] | 165 | |
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[61cada5] | 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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[2f4b430] | 174 | |
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[a95ae9a] | 175 | # reset True change the state of existing button |
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[61cada5] | 176 | self.reset = False |
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[2f4b430] | 177 | |
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[c77d859] | 178 | # flag to allow data2D plot |
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[cfc0913] | 179 | self.enable2D = False |
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[c77d859] | 180 | # model on which the fit would be performed |
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| 181 | self.model = model |
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[93f0a862] | 182 | self.m_name = None |
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[a95ae9a] | 183 | # list of process done to model |
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[dce84c0] | 184 | self.process = [] |
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[a95ae9a] | 185 | # fit page manager |
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[c77d859] | 186 | self.manager = None |
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[a95ae9a] | 187 | # Store the parent of this panel parent |
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[c77d859] | 188 | # For this application fitpanel is the parent |
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[f32d144] | 189 | self.parent = parent |
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[c77d859] | 190 | # Event_owner is the owner of model event |
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| 191 | self.event_owner = None |
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[a95ae9a] | 192 | # page name |
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[cfc0913] | 193 | self.page_name = "" |
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[c8e1996] | 194 | # Contains link between model, its parameters, and panel organization |
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[61cada5] | 195 | self.parameters = [] |
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[fb59ed9] | 196 | # String parameter list that can not be fitted |
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| 197 | self.str_parameters = [] |
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[f32d144] | 198 | # Contains list of parameters that cannot be fitted and reference to |
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[a95ae9a] | 199 | # panel objects |
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[61cada5] | 200 | self.fixed_param = [] |
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[f32d144] | 201 | # Contains list of parameters with dispersity and reference to |
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[a95ae9a] | 202 | # panel objects |
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[61cada5] | 203 | self.fittable_param = [] |
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[a95ae9a] | 204 | # orientation parameters |
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[61cada5] | 205 | self.orientation_params = [] |
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[a95ae9a] | 206 | # orientation parameters for gaussian dispersity |
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[61cada5] | 207 | self.orientation_params_disp = [] |
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[a95ae9a] | 208 | # smearer info |
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[61cada5] | 209 | self.smearer = None |
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[7609f1a] | 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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[db8fd5b] | 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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[a95ae9a] | 217 | # list of dispersion parameters |
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[f32d144] | 218 | self.disp_list = [] |
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[61cada5] | 219 | if self.model is not None: |
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[71f0373] | 220 | self.disp_list = self.model.getDispParamList() |
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[2296316] | 221 | |
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[61cada5] | 222 | self.disp_cb_dict = {} |
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[2296316] | 223 | self.values = {} |
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| 224 | self.weights = {} |
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[2f4b430] | 225 | |
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[a95ae9a] | 226 | # contains link between a model and selected parameters to fit |
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[61cada5] | 227 | self.param_toFit = [] |
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[a95ae9a] | 228 | # dictionary of model type and model class |
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[cfc0913] | 229 | self.model_list_box = None |
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[a95ae9a] | 230 | # save the state of the context menu |
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[61cada5] | 231 | self.saved_states = {} |
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[a95ae9a] | 232 | # save selection of combobox |
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[3b9e023] | 233 | self.formfactorcombobox = None |
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[ea5fa58] | 234 | self.categorycombobox = None |
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[f32d144] | 235 | self.structurecombobox = None |
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[c0ff8cc] | 236 | |
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[a95ae9a] | 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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[b787e68c] | 243 | self.disp_box = 0 |
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[a95ae9a] | 244 | # Qrange |
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| 245 | # Q range |
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[61cada5] | 246 | self.qmin = 0.001 |
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| 247 | self.qmax = 0.1 |
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[a95ae9a] | 248 | # reset data range |
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[0b12abb5] | 249 | self.qmax_x = None |
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| 250 | self.qmin_x = None |
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[2f4b430] | 251 | |
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[cfc0913] | 252 | self.npts = None |
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[61cada5] | 253 | self.name = "" |
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[4523b68] | 254 | self.multi_factor = None |
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[318b5bbb] | 255 | self.magnetic_on = False |
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[a95ae9a] | 256 | # enable smearering state |
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[cfc0913] | 257 | self.enable_smearer = False |
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[fc6ea43] | 258 | self.disable_smearer = True |
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[7609f1a] | 259 | self.pinhole_smearer = False |
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[f32d144] | 260 | self.slit_smearer = False |
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[55bb249c] | 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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[f32d144] | 265 | self.dI_idata = False |
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[a95ae9a] | 266 | # disperity selection |
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[61cada5] | 267 | self.enable_disp = False |
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| 268 | self.disable_disp = True |
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[2f4b430] | 269 | |
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[a95ae9a] | 270 | # state of selected all check button |
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[cfc0913] | 271 | self.cb1 = False |
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[a95ae9a] | 272 | # store value of chisqr |
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[61cada5] | 273 | self.tcChi = None |
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[2f4b430] | 274 | |
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[6f023e8] | 275 | def clone(self): |
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[61cada5] | 276 | """ |
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[5062bbf] | 277 | Create a new copy of the current object |
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[61cada5] | 278 | """ |
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| 279 | model = None |
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| 280 | if self.model is not None: |
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[6f023e8] | 281 | model = self.model.clone() |
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[bb70474] | 282 | model.name = self.model.name |
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[61cada5] | 283 | obj = PageState(self.parent, model=model) |
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| 284 | obj.file = copy.deepcopy(self.file) |
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[6f023e8] | 285 | obj.data = copy.deepcopy(self.data) |
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[61cada5] | 286 | if self.data is not None: |
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| 287 | self.data_name = self.data.name |
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| 288 | obj.data_name = self.data_name |
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| 289 | obj.is_data = self.is_data |
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[dcf29d7] | 290 | obj.model_list_box = copy.deepcopy(self.model_list_box) |
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[2f4b430] | 291 | |
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[ea5fa58] | 292 | obj.categorycombobox = self.categorycombobox |
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[61cada5] | 293 | obj.formfactorcombobox = self.formfactorcombobox |
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[f32d144] | 294 | obj.structurecombobox = self.structurecombobox |
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[2f4b430] | 295 | |
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[a95ae9a] | 296 | # obj.shape_rbutton = self.shape_rbutton |
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| 297 | # obj.shape_indep_rbutton = self.shape_indep_rbutton |
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| 298 | # obj.struct_rbutton = self.struct_rbutton |
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| 299 | # obj.plugin_rbutton = self.plugin_rbutton |
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[2f4b430] | 300 | |
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[dcf29d7] | 301 | obj.manager = self.manager |
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| 302 | obj.event_owner = self.event_owner |
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[71f0373] | 303 | obj.disp_list = copy.deepcopy(self.disp_list) |
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[2f4b430] | 304 | |
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[c477b31] | 305 | obj.enable2D = copy.deepcopy(self.enable2D) |
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[cfc0913] | 306 | obj.parameters = copy.deepcopy(self.parameters) |
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[fb59ed9] | 307 | obj.str_parameters = copy.deepcopy(self.str_parameters) |
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[cfc0913] | 308 | obj.fixed_param = copy.deepcopy(self.fixed_param) |
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| 309 | obj.fittable_param = copy.deepcopy(self.fittable_param) |
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[f32d144] | 310 | obj.orientation_params = copy.deepcopy(self.orientation_params) |
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[c8e1996] | 311 | obj.orientation_params_disp = \ |
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| 312 | copy.deepcopy(self.orientation_params_disp) |
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[b787e68c] | 313 | obj.enable_disp = copy.deepcopy(self.enable_disp) |
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[fc6ea43] | 314 | obj.disable_disp = copy.deepcopy(self.disable_disp) |
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[0aeabc6] | 315 | obj.tcChi = self.tcChi |
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[2f4b430] | 316 | |
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[f32d144] | 317 | if len(self._disp_obj_dict) > 0: |
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| 318 | for k, v in self._disp_obj_dict.iteritems(): |
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| 319 | obj._disp_obj_dict[k] = v |
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| 320 | if len(self.disp_cb_dict) > 0: |
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| 321 | for k, v in self.disp_cb_dict.iteritems(): |
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| 322 | obj.disp_cb_dict[k] = v |
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| 323 | if len(self.values) > 0: |
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| 324 | for k, v in self.values.iteritems(): |
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[2296316] | 325 | obj.values[k] = v |
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[f32d144] | 326 | if len(self.weights) > 0: |
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| 327 | for k, v in self.weights.iteritems(): |
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[2296316] | 328 | obj.weights[k] = v |
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[b787e68c] | 329 | obj.enable_smearer = copy.deepcopy(self.enable_smearer) |
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[fc6ea43] | 330 | obj.disable_smearer = copy.deepcopy(self.disable_smearer) |
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[7609f1a] | 331 | obj.pinhole_smearer = copy.deepcopy(self.pinhole_smearer) |
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| 332 | obj.slit_smearer = copy.deepcopy(self.slit_smearer) |
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| 333 | obj.smear_type = copy.deepcopy(self.smear_type) |
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[55bb249c] | 334 | obj.dI_noweight = copy.deepcopy(self.dI_noweight) |
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| 335 | obj.dI_didata = copy.deepcopy(self.dI_didata) |
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| 336 | obj.dI_sqrdata = copy.deepcopy(self.dI_sqrdata) |
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| 337 | obj.dI_idata = copy.deepcopy(self.dI_idata) |
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[7609f1a] | 338 | obj.dq_l = copy.deepcopy(self.dq_l) |
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| 339 | obj.dq_r = copy.deepcopy(self.dq_r) |
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[db8fd5b] | 340 | obj.dx_max = copy.deepcopy(self.dx_max) |
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| 341 | obj.dx_min = copy.deepcopy(self.dx_min) |
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| 342 | obj.dxl = copy.deepcopy(self.dxl) |
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[2f4b430] | 343 | obj.dxw = copy.deepcopy(self.dxw) |
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[b787e68c] | 344 | obj.disp_box = copy.deepcopy(self.disp_box) |
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| 345 | obj.qmin = copy.deepcopy(self.qmin) |
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| 346 | obj.qmax = copy.deepcopy(self.qmax) |
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[c0ff8cc] | 347 | obj.multi_factor = self.multi_factor |
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[318b5bbb] | 348 | obj.magnetic_on = self.magnetic_on |
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[f32d144] | 349 | obj.npts = copy.deepcopy(self.npts) |
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[b787e68c] | 350 | obj.cb1 = copy.deepcopy(self.cb1) |
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[3370922] | 351 | obj.smearer = copy.deepcopy(self.smearer) |
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[2f4b430] | 352 | |
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[a074145] | 353 | for name, state in self.saved_states.iteritems(): |
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| 354 | copy_name = copy.deepcopy(name) |
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| 355 | copy_state = state.clone() |
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[f32d144] | 356 | obj.saved_states[copy_name] = copy_state |
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[6f023e8] | 357 | return obj |
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[2f4b430] | 358 | |
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[8898558b] | 359 | def _is_sasmodels(self): |
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| 360 | """ |
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| 361 | A check to see if the loaded save state was saved in SasView v4_0+ |
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| 362 | :return: None |
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| 363 | """ |
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| 364 | newname = convert._conversion_target(self.formfactorcombobox) |
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| 365 | if newname == None: |
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| 366 | return True |
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| 367 | else: |
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| 368 | return False |
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| 369 | |
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[3d8c49a] | 370 | def _convert_to_sasmodels(self): |
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| 371 | """ |
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| 372 | Convert parameters to a form usable by sasmodels converter |
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| 373 | |
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| 374 | :return: None |
---|
| 375 | """ |
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| 376 | # Create conversion dictionary to send to sasmodels |
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| 377 | p = dict() |
---|
| 378 | for fittable, name, value, _, uncert, lower, upper, units in \ |
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| 379 | self.parameters: |
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| 380 | if not value: |
---|
| 381 | value = numpy.nan |
---|
| 382 | if not uncert or uncert[1] == '': |
---|
| 383 | uncert[0] = False |
---|
| 384 | uncert[1] = numpy.nan |
---|
| 385 | if not upper or upper[1] == '': |
---|
| 386 | upper[0] = False |
---|
| 387 | upper[1] = numpy.nan |
---|
| 388 | if not lower or lower[1] == '': |
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| 389 | lower[0] = False |
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| 390 | lower[1] = numpy.nan |
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[64c7f39] | 391 | p[name] = float(value) |
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| 392 | p[name + ".fittable"] = bool(fittable) |
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| 393 | p[name + ".std"] = float(uncert[1]) |
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| 394 | p[name + ".upper"] = float(upper[1]) |
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| 395 | p[name + ".lower"] = float(lower[1]) |
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| 396 | p[name + ".units"] = units |
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[377c19a2] | 397 | |
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| 398 | structurefactor, params = \ |
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| 399 | convert.convert_model(self.structurecombobox, p) |
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| 400 | formfactor, params = \ |
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| 401 | convert.convert_model(self.formfactorcombobox, params) |
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[0b1d7d3] | 402 | # if len(self.str_parameters) > 0: |
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| 403 | # formfactor, str_params = \ |
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| 404 | # convert.convert_model(formfactor, self.str_parameters) |
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[3d8c49a] | 405 | |
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| 406 | # Only convert if old != new, otherwise all the same |
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[377c19a2] | 407 | if formfactor != self.formfactorcombobox or \ |
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| 408 | structurefactor != self.structurecombobox: |
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| 409 | self.formfactorcombobox = formfactor |
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| 410 | self.structurecombobox = structurefactor |
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[3d8c49a] | 411 | self.parameters = [] |
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| 412 | for name, info in params.iteritems(): |
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[64c7f39] | 413 | if ".fittable" in name or ".std" in name or ".upper" in name or\ |
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| 414 | ".lower" in name or ".units" in name: |
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| 415 | pass |
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[3d8c49a] | 416 | else: |
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[406644a] | 417 | fittable = params.get(name + ".fittable", True) |
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| 418 | std = params.get(name + ".std", '0.0') |
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| 419 | upper = params.get(name + ".upper", 'inf') |
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| 420 | lower = params.get(name + ".lower", '-inf') |
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[64c7f39] | 421 | units = params.get(name + ".units") |
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[b4fc0f9] | 422 | if std is not None and std is not numpy.nan: |
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[64c7f39] | 423 | std = [True, str(std)] |
---|
| 424 | else: |
---|
| 425 | std = [False, ''] |
---|
[0b1d7d3] | 426 | if lower is not None and lower is not numpy.nan: |
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[64c7f39] | 427 | lower = [True, str(lower)] |
---|
| 428 | else: |
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[0b1d7d3] | 429 | lower = [True, '-inf'] |
---|
| 430 | if upper is not None and upper is not numpy.nan: |
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[64c7f39] | 431 | upper = [True, str(upper)] |
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| 432 | else: |
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[0b1d7d3] | 433 | upper = [True, 'inf'] |
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[64c7f39] | 434 | param_list = [bool(fittable), str(name), str(info), |
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| 435 | "+/-", std, lower, upper, str(units)] |
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| 436 | self.parameters.append(param_list) |
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[3d8c49a] | 437 | |
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| 438 | |
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[61cada5] | 439 | def _repr_helper(self, list, rep): |
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| 440 | """ |
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[5062bbf] | 441 | Helper method to print a state |
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[61cada5] | 442 | """ |
---|
| 443 | for item in list: |
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[f32d144] | 444 | rep += "parameter name: %s \n" % str(item[1]) |
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| 445 | rep += "value: %s\n" % str(item[2]) |
---|
| 446 | rep += "selected: %s\n" % str(item[0]) |
---|
| 447 | rep += "error displayed : %s \n" % str(item[4][0]) |
---|
| 448 | rep += "error value:%s \n" % str(item[4][1]) |
---|
| 449 | rep += "minimum displayed : %s \n" % str(item[5][0]) |
---|
| 450 | rep += "minimum value : %s \n" % str(item[5][1]) |
---|
| 451 | rep += "maximum displayed : %s \n" % str(item[6][0]) |
---|
| 452 | rep += "maximum value : %s \n" % str(item[6][1]) |
---|
| 453 | rep += "parameter unit: %s\n\n" % str(item[7]) |
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[240b9966] | 454 | return rep |
---|
[2f4b430] | 455 | |
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[61cada5] | 456 | def __repr__(self): |
---|
[f32d144] | 457 | """ |
---|
[5062bbf] | 458 | output string for printing |
---|
[11a7e11] | 459 | """ |
---|
[f32d144] | 460 | rep = "\nState name: %s\n" % self.file |
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[11a7e11] | 461 | t = time.localtime(self.timestamp) |
---|
[deff488] | 462 | time_str = time.strftime("%b %d %Y %H;%M;%S ", t) |
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[c0ff8cc] | 463 | |
---|
[f32d144] | 464 | rep += "State created: %s\n" % time_str |
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[998ca90] | 465 | rep += "State form factor combobox selection: %s\n" % \ |
---|
| 466 | self.formfactorcombobox |
---|
| 467 | rep += "State structure factor combobox selection: %s\n" % \ |
---|
| 468 | self.structurecombobox |
---|
[f32d144] | 469 | rep += "is data : %s\n" % self.is_data |
---|
| 470 | rep += "data's name : %s\n" % self.data_name |
---|
| 471 | rep += "data's id : %s\n" % self.data_id |
---|
[a95ae9a] | 472 | if self.model is not None: |
---|
[93f0a862] | 473 | m_name = self.model.__class__.__name__ |
---|
| 474 | if m_name == 'Model': |
---|
| 475 | m_name = self.m_name |
---|
[f32d144] | 476 | rep += "model name : %s\n" % m_name |
---|
[74dc0a4] | 477 | else: |
---|
| 478 | rep += "model name : None\n" |
---|
[f32d144] | 479 | rep += "multi_factor : %s\n" % str(self.multi_factor) |
---|
[2f4b430] | 480 | rep += "magnetic_on : %s\n" % str(self.magnetic_on) |
---|
[ea5fa58] | 481 | rep += "model type (Category) selected: %s\n" % self.categorycombobox |
---|
[f32d144] | 482 | rep += "data : %s\n" % str(self.data) |
---|
[a95ae9a] | 483 | rep += "Plotting Range: min: %s, max: %s, steps: %s\n" % \ |
---|
[c8e1996] | 484 | (str(self.qmin), str(self.qmax), str(self.npts)) |
---|
[f32d144] | 485 | rep += "Dispersion selection : %s\n" % str(self.disp_box) |
---|
| 486 | rep += "Smearing enable : %s\n" % str(self.enable_smearer) |
---|
| 487 | rep += "Smearing disable : %s\n" % str(self.disable_smearer) |
---|
| 488 | rep += "Pinhole smearer enable : %s\n" % str(self.pinhole_smearer) |
---|
| 489 | rep += "Slit smearer enable : %s\n" % str(self.slit_smearer) |
---|
| 490 | rep += "Dispersity enable : %s\n" % str(self.enable_disp) |
---|
| 491 | rep += "Dispersity disable : %s\n" % str(self.disable_disp) |
---|
| 492 | rep += "Slit smearer enable: %s\n" % str(self.slit_smearer) |
---|
[2f4b430] | 493 | |
---|
[f32d144] | 494 | rep += "dI_noweight : %s\n" % str(self.dI_noweight) |
---|
| 495 | rep += "dI_didata : %s\n" % str(self.dI_didata) |
---|
| 496 | rep += "dI_sqrdata : %s\n" % str(self.dI_sqrdata) |
---|
| 497 | rep += "dI_idata : %s\n" % str(self.dI_idata) |
---|
[2f4b430] | 498 | |
---|
[f32d144] | 499 | rep += "2D enable : %s\n" % str(self.enable2D) |
---|
[c8e1996] | 500 | rep += "All parameters checkbox selected: %s\n" % self.cb1 |
---|
[f32d144] | 501 | rep += "Value of Chisqr : %s\n" % str(self.tcChi) |
---|
[c8e1996] | 502 | rep += "Smear object : %s\n" % self.smearer |
---|
| 503 | rep += "Smear type : %s\n" % self.smear_type |
---|
[f32d144] | 504 | rep += "dq_l : %s\n" % self.dq_l |
---|
| 505 | rep += "dq_r : %s\n" % self.dq_r |
---|
[db8fd5b] | 506 | rep += "dx_max : %s\n" % str(self.dx_max) |
---|
[2f4b430] | 507 | rep += "dx_min : %s\n" % str(self.dx_min) |
---|
[db8fd5b] | 508 | rep += "dxl : %s\n" % str(self.dxl) |
---|
[2f4b430] | 509 | rep += "dxw : %s\n" % str(self.dxw) |
---|
[f32d144] | 510 | rep += "model : %s\n\n" % str(self.model) |
---|
[2296316] | 511 | temp_parameters = [] |
---|
| 512 | temp_fittable_param = [] |
---|
| 513 | if self.data.__class__.__name__ == "Data2D": |
---|
| 514 | self.is_2D = True |
---|
| 515 | else: |
---|
| 516 | self.is_2D = False |
---|
| 517 | if self.data is not None: |
---|
| 518 | if not self.is_2D: |
---|
| 519 | for item in self.parameters: |
---|
[a95ae9a] | 520 | if item not in self.orientation_params: |
---|
[2296316] | 521 | temp_parameters.append(item) |
---|
| 522 | for item in self.fittable_param: |
---|
[a95ae9a] | 523 | if item not in self.orientation_params_disp: |
---|
[2296316] | 524 | temp_fittable_param.append(item) |
---|
| 525 | else: |
---|
| 526 | temp_parameters = self.parameters |
---|
| 527 | temp_fittable_param = self.fittable_param |
---|
[2f4b430] | 528 | |
---|
[a95ae9a] | 529 | rep += "number parameters(self.parameters): %s\n" % \ |
---|
| 530 | len(temp_parameters) |
---|
[f32d144] | 531 | rep = self._repr_helper(list=temp_parameters, rep=rep) |
---|
[a95ae9a] | 532 | rep += "number str_parameters(self.str_parameters): %s\n" % \ |
---|
| 533 | len(self.str_parameters) |
---|
[f32d144] | 534 | rep = self._repr_helper(list=self.str_parameters, rep=rep) |
---|
[a95ae9a] | 535 | rep += "number fittable_param(self.fittable_param): %s\n" % \ |
---|
| 536 | len(temp_fittable_param) |
---|
[f32d144] | 537 | rep = self._repr_helper(list=temp_fittable_param, rep=rep) |
---|
[61cada5] | 538 | return rep |
---|
[2296316] | 539 | |
---|
| 540 | def set_report_string(self): |
---|
| 541 | """ |
---|
[f32d144] | 542 | Get the values (strings) from __str__ for report |
---|
[2296316] | 543 | """ |
---|
[d06ae30] | 544 | # Dictionary of the report strings |
---|
[2296316] | 545 | repo_time = "" |
---|
| 546 | model_name = "" |
---|
| 547 | title = "" |
---|
| 548 | title_name = "" |
---|
| 549 | file_name = "" |
---|
| 550 | param_string = "" |
---|
| 551 | paramval_string = "" |
---|
| 552 | chi2_string = "" |
---|
| 553 | q_range = "" |
---|
| 554 | strings = self.__repr__() |
---|
| 555 | lines = strings.split('\n') |
---|
| 556 | |
---|
| 557 | # get all string values from __str__() |
---|
| 558 | for line in lines: |
---|
| 559 | value = "" |
---|
| 560 | content = line.split(":") |
---|
| 561 | name = content[0] |
---|
| 562 | try: |
---|
| 563 | value = content[1] |
---|
[7673ecd] | 564 | except Exception: |
---|
[c8e1996] | 565 | msg = "Report string expected 'name: value' but got %r" % line |
---|
[6c382da] | 566 | logging.error(msg) |
---|
[b7c6a4a] | 567 | if name.count("State created"): |
---|
| 568 | repo_time = "" + value |
---|
[2296316] | 569 | if name.count("parameter name"): |
---|
| 570 | val_name = value.split(".") |
---|
| 571 | if len(val_name) > 1: |
---|
| 572 | if val_name[1].count("width"): |
---|
| 573 | param_string += value + ',' |
---|
| 574 | else: |
---|
| 575 | continue |
---|
| 576 | else: |
---|
| 577 | param_string += value + ',' |
---|
| 578 | if name == "value": |
---|
| 579 | param_string += value + ',' |
---|
[c8e1996] | 580 | fixed_parameter = False |
---|
[b1e609c] | 581 | if name == "selected": |
---|
| 582 | if value == u' False': |
---|
| 583 | fixed_parameter = True |
---|
[2296316] | 584 | if name == "error value": |
---|
[b1e609c] | 585 | if fixed_parameter: |
---|
| 586 | param_string += '(fixed),' |
---|
| 587 | else: |
---|
[d06ae30] | 588 | param_string += value + ',' |
---|
[2296316] | 589 | if name == "parameter unit": |
---|
[f32d144] | 590 | param_string += value + ':' |
---|
[2296316] | 591 | if name == "Value of Chisqr ": |
---|
| 592 | chi2 = ("Chi2/Npts = " + value) |
---|
| 593 | chi2_string = CENTRE % chi2 |
---|
| 594 | if name == "Title": |
---|
| 595 | if len(value.strip()) == 0: |
---|
| 596 | continue |
---|
| 597 | title = value + " [" + repo_time + "]" |
---|
| 598 | title_name = HEADER % title |
---|
| 599 | if name == "data ": |
---|
| 600 | try: |
---|
[b1e609c] | 601 | file_value = ("File name:" + content[2]) |
---|
| 602 | file_name = CENTRE % file_value |
---|
[2296316] | 603 | if len(title) == 0: |
---|
| 604 | title = content[2] + " [" + repo_time + "]" |
---|
| 605 | title_name = HEADER % title |
---|
[7673ecd] | 606 | except Exception: |
---|
[6c382da] | 607 | msg = "While parsing 'data: ...'\n" |
---|
| 608 | logging.error(msg + traceback.format_exc()) |
---|
[74dc0a4] | 609 | if name == "model name ": |
---|
| 610 | try: |
---|
| 611 | modelname = "Model name:" + content[1] |
---|
| 612 | except: |
---|
| 613 | modelname = "Model name:" + " NAN" |
---|
[f32d144] | 614 | model_name = CENTRE % modelname |
---|
[2f4b430] | 615 | |
---|
[2296316] | 616 | if name == "Plotting Range": |
---|
| 617 | try: |
---|
| 618 | q_range = content[1] + " = " + content[2] \ |
---|
| 619 | + " = " + content[3].split(",")[0] |
---|
| 620 | q_name = ("Q Range: " + q_range) |
---|
| 621 | q_range = CENTRE % q_name |
---|
[7673ecd] | 622 | except Exception: |
---|
[6c382da] | 623 | msg = "While parsing 'Plotting Range: ...'\n" |
---|
| 624 | logging.error(msg + traceback.format_exc()) |
---|
[2296316] | 625 | paramval = "" |
---|
[f32d144] | 626 | for lines in param_string.split(":"): |
---|
[2296316] | 627 | line = lines.split(",") |
---|
[f32d144] | 628 | if len(lines) > 0: |
---|
| 629 | param = line[0] |
---|
[2296316] | 630 | param += " = " + line[1] |
---|
| 631 | if len(line[2].split()) > 0 and not line[2].count("None"): |
---|
| 632 | param += " +- " + line[2] |
---|
| 633 | if len(line[3].split()) > 0 and not line[3].count("None"): |
---|
| 634 | param += " " + line[3] |
---|
| 635 | if not paramval.count(param): |
---|
[f32d144] | 636 | paramval += param + "\n" |
---|
[2296316] | 637 | paramval_string += CENTRE % param + "\n" |
---|
[2f4b430] | 638 | |
---|
[a95ae9a] | 639 | text_string = "\n\n\n%s\n\n%s\n%s\n%s\n\n%s" % \ |
---|
| 640 | (title, file, q_name, chi2, paramval) |
---|
[2f4b430] | 641 | |
---|
[f5bdb4a] | 642 | title_name = self._check_html_format(title_name) |
---|
| 643 | file_name = self._check_html_format(file_name) |
---|
| 644 | title = self._check_html_format(title) |
---|
[2f4b430] | 645 | |
---|
[2296316] | 646 | html_string = title_name + "\n" + file_name + \ |
---|
[f32d144] | 647 | "\n" + model_name + \ |
---|
[2296316] | 648 | "\n" + q_range + \ |
---|
| 649 | "\n" + chi2_string + \ |
---|
| 650 | "\n" + ELINE + \ |
---|
| 651 | "\n" + paramval_string + \ |
---|
| 652 | "\n" + ELINE + \ |
---|
| 653 | "\n" + FEET_1 % title + \ |
---|
[f32d144] | 654 | "\n" + FEET_2 |
---|
[2f4b430] | 655 | |
---|
[2296316] | 656 | return html_string, text_string, title |
---|
[2f4b430] | 657 | |
---|
[f5bdb4a] | 658 | def _check_html_format(self, name): |
---|
| 659 | """ |
---|
| 660 | Check string '%' for html format |
---|
| 661 | """ |
---|
| 662 | if name.count('%'): |
---|
| 663 | name = name.replace('%', '%') |
---|
[2f4b430] | 664 | |
---|
[f5bdb4a] | 665 | return name |
---|
[2f4b430] | 666 | |
---|
[2296316] | 667 | def report(self, figs=None, canvases=None): |
---|
| 668 | """ |
---|
| 669 | Invoke report dialog panel |
---|
[2f4b430] | 670 | |
---|
[2296316] | 671 | : param figs: list of pylab figures [list] |
---|
| 672 | """ |
---|
[d85c194] | 673 | from sas.sasgui.perspectives.fitting.report_dialog import ReportDialog |
---|
[2296316] | 674 | # get the strings for report |
---|
| 675 | html_str, text_str, title = self.set_report_string() |
---|
| 676 | # Allow 2 figures to append |
---|
| 677 | if len(figs) == 1: |
---|
[f32d144] | 678 | add_str = FEET_3 |
---|
[2296316] | 679 | elif len(figs) == 2: |
---|
[f32d144] | 680 | add_str = ELINE |
---|
| 681 | add_str += FEET_2 % ("%s") |
---|
| 682 | add_str += ELINE |
---|
| 683 | add_str += FEET_3 |
---|
[2296316] | 684 | elif len(figs) > 2: |
---|
[f32d144] | 685 | add_str = ELINE |
---|
| 686 | add_str += FEET_2 % ("%s") |
---|
| 687 | add_str += ELINE |
---|
| 688 | add_str += FEET_2 % ("%s") |
---|
| 689 | add_str += ELINE |
---|
| 690 | add_str += FEET_3 |
---|
[2296316] | 691 | else: |
---|
| 692 | add_str = "" |
---|
[c0ff8cc] | 693 | |
---|
[2296316] | 694 | # final report html strings |
---|
| 695 | report_str = html_str % ("%s") + add_str |
---|
| 696 | |
---|
| 697 | # make plot image |
---|
| 698 | images = self.set_plot_state(figs, canvases) |
---|
[f32d144] | 699 | report_list = [report_str, text_str, images] |
---|
[6f16e25] | 700 | dialog = ReportDialog(report_list, None, wx.ID_ANY, "") |
---|
[d838715] | 701 | dialog.Show() |
---|
[2f4b430] | 702 | |
---|
[c8e1996] | 703 | def _to_xml_helper(self, thelist, element, newdoc): |
---|
[61cada5] | 704 | """ |
---|
[5062bbf] | 705 | Helper method to create xml file for saving state |
---|
[61cada5] | 706 | """ |
---|
[eddb6ec] | 707 | for item in thelist: |
---|
[61cada5] | 708 | sub_element = newdoc.createElement('parameter') |
---|
| 709 | sub_element.setAttribute('name', str(item[1])) |
---|
| 710 | sub_element.setAttribute('value', str(item[2])) |
---|
| 711 | sub_element.setAttribute('selected_to_fit', str(item[0])) |
---|
| 712 | sub_element.setAttribute('error_displayed', str(item[4][0])) |
---|
| 713 | sub_element.setAttribute('error_value', str(item[4][1])) |
---|
| 714 | sub_element.setAttribute('minimum_displayed', str(item[5][0])) |
---|
| 715 | sub_element.setAttribute('minimum_value', str(item[5][1])) |
---|
| 716 | sub_element.setAttribute('maximum_displayed', str(item[6][0])) |
---|
| 717 | sub_element.setAttribute('maximum_value', str(item[6][1])) |
---|
| 718 | sub_element.setAttribute('unit', str(item[7])) |
---|
| 719 | element.appendChild(sub_element) |
---|
[2f4b430] | 720 | |
---|
[c8e1996] | 721 | def to_xml(self, file="fitting_state.fitv", doc=None, |
---|
| 722 | entry_node=None, batch_fit_state=None): |
---|
[61cada5] | 723 | """ |
---|
[a95ae9a] | 724 | Writes the state of the fit panel to file, as XML. |
---|
[2f4b430] | 725 | |
---|
[5062bbf] | 726 | Compatible with standalone writing, or appending to an |
---|
[998ca90] | 727 | already existing XML document. In that case, the XML document is |
---|
| 728 | required. An optional entry node in the XML document may also be given. |
---|
[2f4b430] | 729 | |
---|
[5062bbf] | 730 | :param file: file to write to |
---|
| 731 | :param doc: XML document object [optional] |
---|
[998ca90] | 732 | :param entry_node: XML node within the XML document at which we |
---|
| 733 | will append the data [optional] |
---|
[c8e1996] | 734 | :param batch_fit_state: simultaneous fit state |
---|
[61cada5] | 735 | """ |
---|
| 736 | from xml.dom.minidom import getDOMImplementation |
---|
[71f0373] | 737 | |
---|
[61cada5] | 738 | # Check whether we have to write a standalone XML file |
---|
| 739 | if doc is None: |
---|
| 740 | impl = getDOMImplementation() |
---|
[f32d144] | 741 | doc_type = impl.createDocumentType(FITTING_NODE_NAME, "1.0", "1.0") |
---|
[61cada5] | 742 | newdoc = impl.createDocument(None, FITTING_NODE_NAME, doc_type) |
---|
| 743 | top_element = newdoc.documentElement |
---|
| 744 | else: |
---|
| 745 | # We are appending to an existing document |
---|
| 746 | newdoc = doc |
---|
[ac5b69d] | 747 | try: |
---|
| 748 | top_element = newdoc.createElement(FITTING_NODE_NAME) |
---|
| 749 | except: |
---|
| 750 | string = etree.tostring(doc, pretty_print=True) |
---|
| 751 | newdoc = parseString(string) |
---|
| 752 | top_element = newdoc.createElement(FITTING_NODE_NAME) |
---|
[61cada5] | 753 | if entry_node is None: |
---|
| 754 | newdoc.documentElement.appendChild(top_element) |
---|
| 755 | else: |
---|
[ac5b69d] | 756 | try: |
---|
| 757 | entry_node.appendChild(top_element) |
---|
| 758 | except: |
---|
| 759 | node_name = entry_node.tag |
---|
| 760 | node_list = newdoc.getElementsByTagName(node_name) |
---|
| 761 | entry_node = node_list.item(0) |
---|
| 762 | entry_node.appendChild(top_element) |
---|
[2f4b430] | 763 | |
---|
[61cada5] | 764 | attr = newdoc.createAttribute("version") |
---|
| 765 | attr.nodeValue = '1.0' |
---|
| 766 | top_element.setAttributeNode(attr) |
---|
[2f4b430] | 767 | |
---|
[61cada5] | 768 | # File name |
---|
| 769 | element = newdoc.createElement("filename") |
---|
| 770 | if self.file is not None: |
---|
| 771 | element.appendChild(newdoc.createTextNode(str(self.file))) |
---|
| 772 | else: |
---|
| 773 | element.appendChild(newdoc.createTextNode(str(file))) |
---|
| 774 | top_element.appendChild(element) |
---|
[2f4b430] | 775 | |
---|
[11a7e11] | 776 | element = newdoc.createElement("timestamp") |
---|
| 777 | element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp))) |
---|
| 778 | attr = newdoc.createAttribute("epoch") |
---|
| 779 | attr.nodeValue = str(self.timestamp) |
---|
| 780 | element.setAttributeNode(attr) |
---|
| 781 | top_element.appendChild(element) |
---|
[a95ae9a] | 782 | |
---|
[61cada5] | 783 | # Inputs |
---|
| 784 | inputs = newdoc.createElement("Attributes") |
---|
| 785 | top_element.appendChild(inputs) |
---|
[2f4b430] | 786 | |
---|
[61cada5] | 787 | if self.data is not None and hasattr(self.data, "group_id"): |
---|
| 788 | self.data_group_id = self.data.group_id |
---|
| 789 | if self.data is not None and hasattr(self.data, "is_data"): |
---|
| 790 | self.is_data = self.data.is_data |
---|
| 791 | if self.data is not None: |
---|
| 792 | self.data_name = self.data.name |
---|
| 793 | if self.data is not None and hasattr(self.data, "id"): |
---|
| 794 | self.data_id = self.data.id |
---|
[2f4b430] | 795 | |
---|
[b1e609c] | 796 | for item in LIST_OF_DATA_ATTRIBUTES: |
---|
[0b12abb5] | 797 | element = newdoc.createElement(item[0]) |
---|
[b1e609c] | 798 | element.setAttribute(item[0], str(getattr(self, item[1]))) |
---|
[f32d144] | 799 | inputs.appendChild(element) |
---|
[2f4b430] | 800 | |
---|
[b1e609c] | 801 | for item in LIST_OF_STATE_ATTRIBUTES: |
---|
[26f3dd5] | 802 | element = newdoc.createElement(item[0]) |
---|
[b1e609c] | 803 | element.setAttribute(item[0], str(getattr(self, item[1]))) |
---|
[26f3dd5] | 804 | inputs.appendChild(element) |
---|
[2f4b430] | 805 | |
---|
[f32d144] | 806 | # For self.values ={ disp_param_name: [vals,...],...} |
---|
| 807 | # and for self.weights ={ disp_param_name: [weights,...],...} |
---|
[b1e609c] | 808 | for item in LIST_OF_MODEL_ATTRIBUTES: |
---|
[11a7e11] | 809 | element = newdoc.createElement(item[0]) |
---|
[b1e609c] | 810 | value_list = getattr(self, item[1]) |
---|
| 811 | for key, value in value_list.iteritems(): |
---|
[2296316] | 812 | sub_element = newdoc.createElement(key) |
---|
| 813 | sub_element.setAttribute('name', str(key)) |
---|
| 814 | for val in value: |
---|
[b1e609c] | 815 | sub_element.appendChild(newdoc.createTextNode(str(val))) |
---|
[2f4b430] | 816 | |
---|
[f32d144] | 817 | element.appendChild(sub_element) |
---|
[11a7e11] | 818 | inputs.appendChild(element) |
---|
[2f4b430] | 819 | |
---|
[2296316] | 820 | # Create doc for the dictionary of self._disp_obj_dic |
---|
[6c382da] | 821 | for tagname, varname, tagtype in DISPERSION_LIST: |
---|
| 822 | element = newdoc.createElement(tagname) |
---|
| 823 | value_list = getattr(self, varname) |
---|
| 824 | for key, value in value_list.iteritems(): |
---|
[f32d144] | 825 | sub_element = newdoc.createElement(key) |
---|
| 826 | sub_element.setAttribute('name', str(key)) |
---|
| 827 | sub_element.setAttribute('value', str(value)) |
---|
| 828 | element.appendChild(sub_element) |
---|
| 829 | inputs.appendChild(element) |
---|
[2f4b430] | 830 | |
---|
[b1e609c] | 831 | for item in LIST_OF_STATE_PARAMETERS: |
---|
[61cada5] | 832 | element = newdoc.createElement(item[0]) |
---|
[c8e1996] | 833 | self._to_xml_helper(thelist=getattr(self, item[1]), |
---|
| 834 | element=element, newdoc=newdoc) |
---|
[61cada5] | 835 | inputs.appendChild(element) |
---|
[2f4b430] | 836 | |
---|
[a95ae9a] | 837 | # Combined and Simultaneous Fit Parameters |
---|
| 838 | if batch_fit_state is not None: |
---|
| 839 | batch_combo = newdoc.createElement('simultaneous_fit') |
---|
| 840 | top_element.appendChild(batch_combo) |
---|
| 841 | |
---|
| 842 | # Simultaneous Fit Number For Linking Later |
---|
| 843 | element = newdoc.createElement('sim_fit_number') |
---|
| 844 | element.setAttribute('fit_number', str(batch_fit_state.fit_page_no)) |
---|
| 845 | batch_combo.appendChild(element) |
---|
| 846 | |
---|
| 847 | # Save constraints |
---|
| 848 | constraints = newdoc.createElement('constraints') |
---|
| 849 | batch_combo.appendChild(constraints) |
---|
| 850 | for constraint in batch_fit_state.constraints_list: |
---|
[998ca90] | 851 | if constraint.model_cbox.GetValue() != "": |
---|
[c8e1996] | 852 | # model_cbox, param_cbox, egal_txt, constraint, |
---|
| 853 | # btRemove, sizer |
---|
[998ca90] | 854 | doc_cons = newdoc.createElement('constraint') |
---|
| 855 | doc_cons.setAttribute('model_cbox', |
---|
| 856 | str(constraint.model_cbox.GetValue())) |
---|
| 857 | doc_cons.setAttribute('param_cbox', |
---|
| 858 | str(constraint.param_cbox.GetValue())) |
---|
| 859 | doc_cons.setAttribute('egal_txt', |
---|
| 860 | str(constraint.egal_txt.GetLabel())) |
---|
| 861 | doc_cons.setAttribute('constraint', |
---|
| 862 | str(constraint.constraint.GetValue())) |
---|
| 863 | constraints.appendChild(doc_cons) |
---|
[a95ae9a] | 864 | |
---|
| 865 | # Save all models |
---|
| 866 | models = newdoc.createElement('model_list') |
---|
| 867 | batch_combo.appendChild(models) |
---|
| 868 | for model in batch_fit_state.model_list: |
---|
| 869 | doc_model = newdoc.createElement('model_list_item') |
---|
| 870 | doc_model.setAttribute('checked', str(model[0].GetValue())) |
---|
| 871 | keys = model[1].keys() |
---|
| 872 | doc_model.setAttribute('name', str(keys[0])) |
---|
| 873 | values = model[1].get(keys[0]) |
---|
| 874 | doc_model.setAttribute('fit_number', str(model[2])) |
---|
| 875 | doc_model.setAttribute('fit_page_source', str(model[3])) |
---|
| 876 | doc_model.setAttribute('model_name', str(values.model.id)) |
---|
| 877 | models.appendChild(doc_model) |
---|
| 878 | |
---|
| 879 | # Select All Checkbox |
---|
| 880 | element = newdoc.createElement('select_all') |
---|
| 881 | if batch_fit_state.select_all: |
---|
| 882 | element.setAttribute('checked', 'True') |
---|
| 883 | else: |
---|
| 884 | element.setAttribute('checked', 'False') |
---|
| 885 | batch_combo.appendChild(element) |
---|
| 886 | |
---|
[61cada5] | 887 | # Save the file |
---|
| 888 | if doc is None: |
---|
| 889 | fd = open(file, 'w') |
---|
| 890 | fd.write(newdoc.toprettyxml()) |
---|
| 891 | fd.close() |
---|
| 892 | return None |
---|
| 893 | else: |
---|
[ac5b69d] | 894 | return newdoc |
---|
[2f4b430] | 895 | |
---|
[c8e1996] | 896 | def _from_xml_helper(self, node, list): |
---|
[61cada5] | 897 | """ |
---|
[5062bbf] | 898 | Helper function to write state to xml |
---|
[61cada5] | 899 | """ |
---|
| 900 | for item in node: |
---|
[0b12abb5] | 901 | try: |
---|
| 902 | name = item.get('name') |
---|
| 903 | except: |
---|
| 904 | name = None |
---|
| 905 | try: |
---|
| 906 | value = item.get('value') |
---|
| 907 | except: |
---|
| 908 | value = None |
---|
| 909 | try: |
---|
[3ad91de] | 910 | selected_to_fit = (item.get('selected_to_fit') == "True") |
---|
[0b12abb5] | 911 | except: |
---|
| 912 | selected_to_fit = None |
---|
| 913 | try: |
---|
[3ad91de] | 914 | error_displayed = (item.get('error_displayed') == "True") |
---|
[0b12abb5] | 915 | except: |
---|
| 916 | error_displayed = None |
---|
[f32d144] | 917 | try: |
---|
[0b12abb5] | 918 | error_value = item.get('error_value') |
---|
| 919 | except: |
---|
| 920 | error_value = None |
---|
| 921 | try: |
---|
[f32d144] | 922 | minimum_displayed = (item.get('minimum_displayed') == "True") |
---|
[0b12abb5] | 923 | except: |
---|
| 924 | minimum_displayed = None |
---|
| 925 | try: |
---|
| 926 | minimum_value = item.get('minimum_value') |
---|
| 927 | except: |
---|
| 928 | minimum_value = None |
---|
| 929 | try: |
---|
[3ad91de] | 930 | maximum_displayed = (item.get('maximum_displayed') == "True") |
---|
[0b12abb5] | 931 | except: |
---|
| 932 | maximum_displayed = None |
---|
| 933 | try: |
---|
| 934 | maximum_value = item.get('maximum_value') |
---|
| 935 | except: |
---|
| 936 | maximum_value = None |
---|
| 937 | try: |
---|
| 938 | unit = item.get('unit') |
---|
| 939 | except: |
---|
| 940 | unit = None |
---|
[2296316] | 941 | list.append([selected_to_fit, name, value, "+/-", |
---|
| 942 | [error_displayed, error_value], |
---|
[f32d144] | 943 | [minimum_displayed, minimum_value], |
---|
| 944 | [maximum_displayed, maximum_value], unit]) |
---|
[2f4b430] | 945 | |
---|
[c8e1996] | 946 | def from_xml(self, file=None, node=None): |
---|
[61cada5] | 947 | """ |
---|
[5062bbf] | 948 | Load fitting state from a file |
---|
[2f4b430] | 949 | |
---|
[5062bbf] | 950 | :param file: .fitv file |
---|
| 951 | :param node: node of a XML document to read from |
---|
[61cada5] | 952 | """ |
---|
| 953 | if file is not None: |
---|
[11a7e11] | 954 | msg = "PageState no longer supports non-CanSAS" |
---|
| 955 | msg += " format for fitting files" |
---|
| 956 | raise RuntimeError, msg |
---|
[2f4b430] | 957 | |
---|
[e89aed5] | 958 | if node.get('version') and node.get('version') == '1.0': |
---|
[2f4b430] | 959 | |
---|
[61cada5] | 960 | # Get file name |
---|
| 961 | entry = get_content('ns:filename', node) |
---|
| 962 | if entry is not None: |
---|
| 963 | self.file = entry.text.strip() |
---|
[2f4b430] | 964 | |
---|
[11a7e11] | 965 | # Get time stamp |
---|
| 966 | entry = get_content('ns:timestamp', node) |
---|
| 967 | if entry is not None and entry.get('epoch'): |
---|
| 968 | try: |
---|
| 969 | self.timestamp = float(entry.get('epoch')) |
---|
| 970 | except: |
---|
| 971 | msg = "PageState.fromXML: Could not" |
---|
| 972 | msg += " read timestamp\n %s" % sys.exc_value |
---|
| 973 | logging.error(msg) |
---|
[2f4b430] | 974 | |
---|
[61cada5] | 975 | if entry is not None: |
---|
[c8e1996] | 976 | # Parse fitting attributes |
---|
| 977 | entry = get_content('ns:Attributes', node) |
---|
| 978 | for item in LIST_OF_DATA_ATTRIBUTES: |
---|
| 979 | node = get_content('ns:%s' % item[0], entry) |
---|
| 980 | setattr(self, item[0], parse_entry_helper(node, item)) |
---|
| 981 | |
---|
[b1e609c] | 982 | for item in LIST_OF_STATE_ATTRIBUTES: |
---|
[2296316] | 983 | node = get_content('ns:%s' % item[0], entry) |
---|
[b1e609c] | 984 | setattr(self, item[0], parse_entry_helper(node, item)) |
---|
[2f4b430] | 985 | |
---|
[b1e609c] | 986 | for item in LIST_OF_STATE_PARAMETERS: |
---|
[2296316] | 987 | node = get_content("ns:%s" % item[0], entry) |
---|
[c8e1996] | 988 | self._from_xml_helper(node=node, |
---|
| 989 | list=getattr(self, item[1])) |
---|
[2f4b430] | 990 | |
---|
[f32d144] | 991 | # Recover _disp_obj_dict from xml file |
---|
| 992 | self._disp_obj_dict = {} |
---|
[6c382da] | 993 | for tagname, varname, tagtype in DISPERSION_LIST: |
---|
| 994 | node = get_content("ns:%s" % tagname, entry) |
---|
[2296316] | 995 | for attr in node: |
---|
[6c382da] | 996 | parameter = str(attr.get('name')) |
---|
| 997 | value = attr.get('value') |
---|
| 998 | if value.startswith("<"): |
---|
| 999 | try: |
---|
| 1000 | # <path.to.NamedDistribution object/instance...> |
---|
| 1001 | cls_name = value[1:].split()[0].split('.')[-1] |
---|
| 1002 | cls = getattr(sasmodels.weights, cls_name) |
---|
| 1003 | value = cls.type |
---|
| 1004 | except Exception: |
---|
[998ca90] | 1005 | base = "unable to load distribution %r for %s" |
---|
| 1006 | logging.error(base % (value, parameter)) |
---|
[6c382da] | 1007 | continue |
---|
| 1008 | _disp_obj_dict = getattr(self, varname) |
---|
| 1009 | _disp_obj_dict[parameter] = value |
---|
[2f4b430] | 1010 | |
---|
[f32d144] | 1011 | # get self.values and self.weights dic. if exists |
---|
[6c382da] | 1012 | for tagname, varname in LIST_OF_MODEL_ATTRIBUTES: |
---|
| 1013 | node = get_content("ns:%s" % tagname, entry) |
---|
[2296316] | 1014 | dic = {} |
---|
[b1e609c] | 1015 | value_list = [] |
---|
[2296316] | 1016 | for par in node: |
---|
| 1017 | name = par.get('name') |
---|
[6c382da] | 1018 | values = par.text.split() |
---|
[2296316] | 1019 | # Get lines only with numbers |
---|
| 1020 | for line in values: |
---|
| 1021 | try: |
---|
[f32d144] | 1022 | val = float(line) |
---|
[b1e609c] | 1023 | value_list.append(val) |
---|
[7673ecd] | 1024 | except Exception: |
---|
[2296316] | 1025 | # pass if line is empty (it happens) |
---|
[6c382da] | 1026 | msg = ("Error reading %r from %s %s\n" |
---|
| 1027 | % (line, tagname, name)) |
---|
| 1028 | logging.error(msg + traceback.format_exc()) |
---|
[0e33a8d] | 1029 | dic[name] = numpy.array(value_list) |
---|
[6c382da] | 1030 | setattr(self, varname, dic) |
---|
[2f4b430] | 1031 | |
---|
[2296316] | 1032 | def set_plot_state(self, figs, canvases): |
---|
| 1033 | """ |
---|
| 1034 | Build image state that wx.html understand |
---|
| 1035 | by plotting, putting it into wx.FileSystem image object |
---|
| 1036 | |
---|
| 1037 | """ |
---|
| 1038 | images = [] |
---|
| 1039 | |
---|
| 1040 | # Reset memory |
---|
| 1041 | self.imgRAM = None |
---|
| 1042 | wx.MemoryFSHandler() |
---|
[2f4b430] | 1043 | |
---|
[2296316] | 1044 | # For no figures in the list, prepare empty plot |
---|
[c8e1996] | 1045 | if figs is None or len(figs) == 0: |
---|
[2296316] | 1046 | figs = [None] |
---|
[2f4b430] | 1047 | |
---|
[f32d144] | 1048 | # Loop over the list of figures |
---|
[2296316] | 1049 | # use wx.MemoryFSHandler |
---|
[f32d144] | 1050 | self.imgRAM = wx.MemoryFSHandler() |
---|
[2296316] | 1051 | for fig in figs: |
---|
[c8e1996] | 1052 | if fig is not None: |
---|
[2296316] | 1053 | ind = figs.index(fig) |
---|
| 1054 | canvas = canvases[ind] |
---|
[2f4b430] | 1055 | |
---|
[c8e1996] | 1056 | # store the image in wx.FileSystem Object |
---|
[2296316] | 1057 | wx.FileSystem.AddHandler(wx.MemoryFSHandler()) |
---|
[2f4b430] | 1058 | |
---|
[2296316] | 1059 | # index of the fig |
---|
| 1060 | ind = figs.index(fig) |
---|
[2f4b430] | 1061 | |
---|
[c8e1996] | 1062 | # AddFile, image can be retrieved with 'memory:filename' |
---|
[f32d144] | 1063 | self.imgRAM.AddFile('img_fit%s.png' % ind, |
---|
[2296316] | 1064 | canvas.bitmap, wx.BITMAP_TYPE_PNG) |
---|
[2f4b430] | 1065 | |
---|
[c8e1996] | 1066 | # append figs |
---|
[2296316] | 1067 | images.append(fig) |
---|
[2f4b430] | 1068 | |
---|
[c0ff8cc] | 1069 | return images |
---|
[61cada5] | 1070 | |
---|
[f32d144] | 1071 | |
---|
[61cada5] | 1072 | class Reader(CansasReader): |
---|
| 1073 | """ |
---|
[5062bbf] | 1074 | Class to load a .fitv fitting file |
---|
[61cada5] | 1075 | """ |
---|
[c8e1996] | 1076 | # File type |
---|
[61cada5] | 1077 | type_name = "Fitting" |
---|
[2f4b430] | 1078 | |
---|
[c8e1996] | 1079 | # Wildcards |
---|
[b35d3d1] | 1080 | type = ["Fitting files (*.fitv)|*.fitv" |
---|
[b9a5f0e] | 1081 | "SASView file (*.svs)|*.svs"] |
---|
[c8e1996] | 1082 | # List of allowed extensions |
---|
[f32d144] | 1083 | ext = ['.fitv', '.FITV', '.svs', 'SVS'] |
---|
[2f4b430] | 1084 | |
---|
[61cada5] | 1085 | def __init__(self, call_back=None, cansas=True): |
---|
[df7ed14] | 1086 | CansasReader.__init__(self) |
---|
[61cada5] | 1087 | """ |
---|
[5062bbf] | 1088 | Initialize the call-back method to be called |
---|
| 1089 | after we load a file |
---|
[2f4b430] | 1090 | |
---|
[5062bbf] | 1091 | :param call_back: call-back method |
---|
| 1092 | :param cansas: True = files will be written/read in CanSAS format |
---|
| 1093 | False = write CanSAS format |
---|
[2f4b430] | 1094 | |
---|
[61cada5] | 1095 | """ |
---|
[c8e1996] | 1096 | # Call back method to be executed after a file is read |
---|
[61cada5] | 1097 | self.call_back = call_back |
---|
[c8e1996] | 1098 | # CanSAS format flag |
---|
[61cada5] | 1099 | self.cansas = cansas |
---|
[75fbd17] | 1100 | self.state = None |
---|
[a95ae9a] | 1101 | # batch fitting params for saving |
---|
| 1102 | self.batchfit_params = [] |
---|
[2f4b430] | 1103 | |
---|
[75fbd17] | 1104 | def get_state(self): |
---|
| 1105 | return self.state |
---|
[2f4b430] | 1106 | |
---|
[61cada5] | 1107 | def read(self, path): |
---|
[f32d144] | 1108 | """ |
---|
[5062bbf] | 1109 | Load a new P(r) inversion state from file |
---|
[2f4b430] | 1110 | |
---|
[5062bbf] | 1111 | :param path: file path |
---|
[2f4b430] | 1112 | |
---|
[61cada5] | 1113 | """ |
---|
[c8e1996] | 1114 | if self.cansas: |
---|
[61cada5] | 1115 | return self._read_cansas(path) |
---|
[2f4b430] | 1116 | |
---|
[e9b12eaf] | 1117 | def _data2d_to_xml_doc(self, datainfo): |
---|
[61cada5] | 1118 | """ |
---|
[5062bbf] | 1119 | Create an XML document to contain the content of a Data2D |
---|
[2f4b430] | 1120 | |
---|
[5062bbf] | 1121 | :param datainfo: Data2D object |
---|
[2f4b430] | 1122 | |
---|
[61cada5] | 1123 | """ |
---|
| 1124 | if not issubclass(datainfo.__class__, Data2D): |
---|
| 1125 | raise RuntimeError, "The cansas writer expects a Data2D instance" |
---|
[2f4b430] | 1126 | |
---|
[998ca90] | 1127 | title = "cansas1d/%s" % self.version |
---|
| 1128 | title += "http://svn.smallangles.net/svn/canSAS/1dwg/trunk/cansas1d.xsd" |
---|
[61cada5] | 1129 | doc = xml.dom.minidom.Document() |
---|
| 1130 | main_node = doc.createElement("SASroot") |
---|
| 1131 | main_node.setAttribute("version", self.version) |
---|
[df7ed14] | 1132 | main_node.setAttribute("xmlns", "cansas1d/%s" % self.version) |
---|
[998ca90] | 1133 | main_node.setAttribute("xmlns:xsi", |
---|
| 1134 | "http://www.w3.org/2001/XMLSchema-instance") |
---|
| 1135 | main_node.setAttribute("xsi:schemaLocation", title) |
---|
[2f4b430] | 1136 | |
---|
[61cada5] | 1137 | doc.appendChild(main_node) |
---|
[2f4b430] | 1138 | |
---|
[61cada5] | 1139 | entry_node = doc.createElement("SASentry") |
---|
| 1140 | main_node.appendChild(entry_node) |
---|
[2f4b430] | 1141 | |
---|
[61cada5] | 1142 | write_node(doc, entry_node, "Title", datainfo.title) |
---|
[df7ed14] | 1143 | if datainfo is not None: |
---|
[998ca90] | 1144 | write_node(doc, entry_node, "data_class", |
---|
| 1145 | datainfo.__class__.__name__) |
---|
[61cada5] | 1146 | for item in datainfo.run: |
---|
| 1147 | runname = {} |
---|
[c8e1996] | 1148 | if item in datainfo.run_name and \ |
---|
[998ca90] | 1149 | len(str(datainfo.run_name[item])) > 1: |
---|
[b1e609c] | 1150 | runname = {'name': datainfo.run_name[item]} |
---|
[61cada5] | 1151 | write_node(doc, entry_node, "Run", item, runname) |
---|
| 1152 | # Data info |
---|
[df7ed14] | 1153 | new_node = doc.createElement("SASdata") |
---|
| 1154 | entry_node.appendChild(new_node) |
---|
[b1e609c] | 1155 | for item in LIST_OF_DATA_2D_ATTR: |
---|
[e9b12eaf] | 1156 | element = doc.createElement(item[0]) |
---|
[b1e609c] | 1157 | element.setAttribute(item[0], str(getattr(datainfo, item[1]))) |
---|
[df7ed14] | 1158 | new_node.appendChild(element) |
---|
[2f4b430] | 1159 | |
---|
[b1e609c] | 1160 | for item in LIST_OF_DATA_2D_VALUES: |
---|
[df7ed14] | 1161 | root_node = doc.createElement(item[0]) |
---|
| 1162 | new_node.appendChild(root_node) |
---|
[b1e609c] | 1163 | temp_list = getattr(datainfo, item[1]) |
---|
[df7ed14] | 1164 | |
---|
[2f4b430] | 1165 | if temp_list is None or len(temp_list) == 0: |
---|
[df7ed14] | 1166 | element = doc.createElement(item[0]) |
---|
[b1e609c] | 1167 | element.appendChild(doc.createTextNode(str(temp_list))) |
---|
[df7ed14] | 1168 | root_node.appendChild(element) |
---|
[35b556d] | 1169 | else: |
---|
| 1170 | for value in temp_list: |
---|
[df7ed14] | 1171 | element = doc.createElement(item[0]) |
---|
[b1e609c] | 1172 | element.setAttribute(item[0], str(value)) |
---|
[df7ed14] | 1173 | root_node.appendChild(element) |
---|
[2f4b430] | 1174 | |
---|
[61cada5] | 1175 | # Sample info |
---|
| 1176 | sample = doc.createElement("SASsample") |
---|
| 1177 | if datainfo.sample.name is not None: |
---|
| 1178 | sample.setAttribute("name", str(datainfo.sample.name)) |
---|
| 1179 | entry_node.appendChild(sample) |
---|
| 1180 | write_node(doc, sample, "ID", str(datainfo.sample.ID)) |
---|
[f32d144] | 1181 | write_node(doc, sample, "thickness", datainfo.sample.thickness, |
---|
| 1182 | {"unit": datainfo.sample.thickness_unit}) |
---|
[61cada5] | 1183 | write_node(doc, sample, "transmission", datainfo.sample.transmission) |
---|
[f32d144] | 1184 | write_node(doc, sample, "temperature", datainfo.sample.temperature, |
---|
| 1185 | {"unit": datainfo.sample.temperature_unit}) |
---|
[2f4b430] | 1186 | |
---|
[61cada5] | 1187 | for item in datainfo.sample.details: |
---|
| 1188 | write_node(doc, sample, "details", item) |
---|
[2f4b430] | 1189 | |
---|
[61cada5] | 1190 | pos = doc.createElement("position") |
---|
[f32d144] | 1191 | written = write_node(doc, pos, "x", datainfo.sample.position.x, |
---|
| 1192 | {"unit": datainfo.sample.position_unit}) |
---|
| 1193 | written = written | write_node(doc, pos, "y", |
---|
| 1194 | datainfo.sample.position.y, |
---|
| 1195 | {"unit": datainfo.sample.position_unit}) |
---|
| 1196 | written = written | write_node(doc, pos, "z", |
---|
| 1197 | datainfo.sample.position.z, |
---|
| 1198 | {"unit": datainfo.sample.position_unit}) |
---|
[c8e1996] | 1199 | if written: |
---|
[61cada5] | 1200 | sample.appendChild(pos) |
---|
[2f4b430] | 1201 | |
---|
[61cada5] | 1202 | ori = doc.createElement("orientation") |
---|
[f32d144] | 1203 | written = write_node(doc, ori, "roll", datainfo.sample.orientation.x, |
---|
| 1204 | {"unit": datainfo.sample.orientation_unit}) |
---|
| 1205 | written = written | write_node(doc, ori, "pitch", |
---|
| 1206 | datainfo.sample.orientation.y, |
---|
[c8e1996] | 1207 | {"unit": |
---|
| 1208 | datainfo.sample.orientation_unit}) |
---|
[f32d144] | 1209 | written = written | write_node(doc, ori, "yaw", |
---|
| 1210 | datainfo.sample.orientation.z, |
---|
[c8e1996] | 1211 | {"unit": |
---|
| 1212 | datainfo.sample.orientation_unit}) |
---|
| 1213 | if written: |
---|
[61cada5] | 1214 | sample.appendChild(ori) |
---|
[2f4b430] | 1215 | |
---|
[61cada5] | 1216 | # Instrument info |
---|
| 1217 | instr = doc.createElement("SASinstrument") |
---|
| 1218 | entry_node.appendChild(instr) |
---|
[2f4b430] | 1219 | |
---|
[61cada5] | 1220 | write_node(doc, instr, "name", datainfo.instrument) |
---|
[2f4b430] | 1221 | |
---|
[61cada5] | 1222 | # Source |
---|
| 1223 | source = doc.createElement("SASsource") |
---|
| 1224 | if datainfo.source.name is not None: |
---|
| 1225 | source.setAttribute("name", str(datainfo.source.name)) |
---|
| 1226 | instr.appendChild(source) |
---|
[2f4b430] | 1227 | |
---|
[61cada5] | 1228 | write_node(doc, source, "radiation", datainfo.source.radiation) |
---|
| 1229 | write_node(doc, source, "beam_shape", datainfo.source.beam_shape) |
---|
| 1230 | size = doc.createElement("beam_size") |
---|
| 1231 | if datainfo.source.beam_size_name is not None: |
---|
| 1232 | size.setAttribute("name", str(datainfo.source.beam_size_name)) |
---|
[f32d144] | 1233 | written = write_node(doc, size, "x", datainfo.source.beam_size.x, |
---|
| 1234 | {"unit": datainfo.source.beam_size_unit}) |
---|
| 1235 | written = written | write_node(doc, size, "y", |
---|
| 1236 | datainfo.source.beam_size.y, |
---|
| 1237 | {"unit": datainfo.source.beam_size_unit}) |
---|
| 1238 | written = written | write_node(doc, size, "z", |
---|
| 1239 | datainfo.source.beam_size.z, |
---|
| 1240 | {"unit": datainfo.source.beam_size_unit}) |
---|
[c8e1996] | 1241 | if written: |
---|
[61cada5] | 1242 | source.appendChild(size) |
---|
[2f4b430] | 1243 | |
---|
[f32d144] | 1244 | write_node(doc, source, "wavelength", datainfo.source.wavelength, |
---|
| 1245 | {"unit": datainfo.source.wavelength_unit}) |
---|
| 1246 | write_node(doc, source, "wavelength_min", |
---|
| 1247 | datainfo.source.wavelength_min, |
---|
| 1248 | {"unit": datainfo.source.wavelength_min_unit}) |
---|
| 1249 | write_node(doc, source, "wavelength_max", |
---|
| 1250 | datainfo.source.wavelength_max, |
---|
| 1251 | {"unit": datainfo.source.wavelength_max_unit}) |
---|
| 1252 | write_node(doc, source, "wavelength_spread", |
---|
| 1253 | datainfo.source.wavelength_spread, |
---|
| 1254 | {"unit": datainfo.source.wavelength_spread_unit}) |
---|
[2f4b430] | 1255 | |
---|
[61cada5] | 1256 | # Collimation |
---|
| 1257 | for item in datainfo.collimation: |
---|
| 1258 | coll = doc.createElement("SAScollimation") |
---|
| 1259 | if item.name is not None: |
---|
| 1260 | coll.setAttribute("name", str(item.name)) |
---|
| 1261 | instr.appendChild(coll) |
---|
[2f4b430] | 1262 | |
---|
[f32d144] | 1263 | write_node(doc, coll, "length", item.length, |
---|
| 1264 | {"unit": item.length_unit}) |
---|
[2f4b430] | 1265 | |
---|
[61cada5] | 1266 | for apert in item.aperture: |
---|
| 1267 | ap = doc.createElement("aperture") |
---|
| 1268 | if apert.name is not None: |
---|
| 1269 | ap.setAttribute("name", str(apert.name)) |
---|
| 1270 | if apert.type is not None: |
---|
| 1271 | ap.setAttribute("type", str(apert.type)) |
---|
| 1272 | coll.appendChild(ap) |
---|
[2f4b430] | 1273 | |
---|
[f32d144] | 1274 | write_node(doc, ap, "distance", apert.distance, |
---|
| 1275 | {"unit": apert.distance_unit}) |
---|
[2f4b430] | 1276 | |
---|
[61cada5] | 1277 | size = doc.createElement("size") |
---|
| 1278 | if apert.size_name is not None: |
---|
| 1279 | size.setAttribute("name", str(apert.size_name)) |
---|
[f32d144] | 1280 | written = write_node(doc, size, "x", apert.size.x, |
---|
| 1281 | {"unit": apert.size_unit}) |
---|
| 1282 | written = written | write_node(doc, size, "y", apert.size.y, |
---|
| 1283 | {"unit": apert.size_unit}) |
---|
| 1284 | written = written | write_node(doc, size, "z", apert.size.z, |
---|
| 1285 | {"unit": apert.size_unit}) |
---|
[c8e1996] | 1286 | if written: |
---|
[61cada5] | 1287 | ap.appendChild(size) |
---|
| 1288 | |
---|
| 1289 | # Detectors |
---|
| 1290 | for item in datainfo.detector: |
---|
| 1291 | det = doc.createElement("SASdetector") |
---|
| 1292 | written = write_node(doc, det, "name", item.name) |
---|
[f32d144] | 1293 | written = written | write_node(doc, det, "SDD", item.distance, |
---|
| 1294 | {"unit": item.distance_unit}) |
---|
| 1295 | written = written | write_node(doc, det, "slit_length", |
---|
| 1296 | item.slit_length, |
---|
| 1297 | {"unit": item.slit_length_unit}) |
---|
[c8e1996] | 1298 | if written: |
---|
[61cada5] | 1299 | instr.appendChild(det) |
---|
[2f4b430] | 1300 | |
---|
[61cada5] | 1301 | off = doc.createElement("offset") |
---|
[f32d144] | 1302 | written = write_node(doc, off, "x", item.offset.x, |
---|
| 1303 | {"unit": item.offset_unit}) |
---|
| 1304 | written = written | write_node(doc, off, "y", item.offset.y, |
---|
| 1305 | {"unit": item.offset_unit}) |
---|
| 1306 | written = written | write_node(doc, off, "z", item.offset.z, |
---|
| 1307 | {"unit": item.offset_unit}) |
---|
[c8e1996] | 1308 | if written: |
---|
[61cada5] | 1309 | det.appendChild(off) |
---|
[2f4b430] | 1310 | |
---|
[61cada5] | 1311 | center = doc.createElement("beam_center") |
---|
[f32d144] | 1312 | written = write_node(doc, center, "x", item.beam_center.x, |
---|
| 1313 | {"unit": item.beam_center_unit}) |
---|
| 1314 | written = written | write_node(doc, center, "y", |
---|
| 1315 | item.beam_center.y, |
---|
| 1316 | {"unit": item.beam_center_unit}) |
---|
| 1317 | written = written | write_node(doc, center, "z", |
---|
| 1318 | item.beam_center.z, |
---|
| 1319 | {"unit": item.beam_center_unit}) |
---|
[c8e1996] | 1320 | if written: |
---|
[61cada5] | 1321 | det.appendChild(center) |
---|
[2f4b430] | 1322 | |
---|
[61cada5] | 1323 | pix = doc.createElement("pixel_size") |
---|
[f32d144] | 1324 | written = write_node(doc, pix, "x", item.pixel_size.x, |
---|
| 1325 | {"unit": item.pixel_size_unit}) |
---|
| 1326 | written = written | write_node(doc, pix, "y", item.pixel_size.y, |
---|
| 1327 | {"unit": item.pixel_size_unit}) |
---|
| 1328 | written = written | write_node(doc, pix, "z", item.pixel_size.z, |
---|
| 1329 | {"unit": item.pixel_size_unit}) |
---|
[c8e1996] | 1330 | if written: |
---|
[61cada5] | 1331 | det.appendChild(pix) |
---|
[2f4b430] | 1332 | |
---|
[61cada5] | 1333 | ori = doc.createElement("orientation") |
---|
[f32d144] | 1334 | written = write_node(doc, ori, "roll", item.orientation.x, |
---|
| 1335 | {"unit": item.orientation_unit}) |
---|
| 1336 | written = written | write_node(doc, ori, "pitch", |
---|
| 1337 | item.orientation.y, |
---|
| 1338 | {"unit": item.orientation_unit}) |
---|
| 1339 | written = written | write_node(doc, ori, "yaw", item.orientation.z, |
---|
| 1340 | {"unit": item.orientation_unit}) |
---|
[c8e1996] | 1341 | if written: |
---|
[61cada5] | 1342 | det.appendChild(ori) |
---|
[2f4b430] | 1343 | |
---|
[61cada5] | 1344 | # Processes info |
---|
| 1345 | for item in datainfo.process: |
---|
| 1346 | node = doc.createElement("SASprocess") |
---|
| 1347 | entry_node.appendChild(node) |
---|
| 1348 | |
---|
| 1349 | write_node(doc, node, "name", item.name) |
---|
| 1350 | write_node(doc, node, "date", item.date) |
---|
| 1351 | write_node(doc, node, "description", item.description) |
---|
| 1352 | for term in item.term: |
---|
| 1353 | value = term['value'] |
---|
| 1354 | del term['value'] |
---|
| 1355 | write_node(doc, node, "term", value, term) |
---|
| 1356 | for note in item.notes: |
---|
| 1357 | write_node(doc, node, "SASprocessnote", note) |
---|
| 1358 | # Return the document, and the SASentry node associated with |
---|
| 1359 | # the data we just wrote |
---|
| 1360 | return doc, entry_node |
---|
[2f4b430] | 1361 | |
---|
[61cada5] | 1362 | def _parse_state(self, entry): |
---|
| 1363 | """ |
---|
[5062bbf] | 1364 | Read a fit result from an XML node |
---|
[2f4b430] | 1365 | |
---|
[f32d144] | 1366 | :param entry: XML node to read from |
---|
[5062bbf] | 1367 | :return: PageState object |
---|
[61cada5] | 1368 | """ |
---|
| 1369 | # Create an empty state |
---|
[2f4b430] | 1370 | state = None |
---|
[61cada5] | 1371 | # Locate the P(r) node |
---|
| 1372 | try: |
---|
[f32d144] | 1373 | nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, |
---|
| 1374 | namespaces={'ns': CANSAS_NS}) |
---|
[e89aed5] | 1375 | if nodes: |
---|
[b35d3d1] | 1376 | # Create an empty state |
---|
[f32d144] | 1377 | state = PageState() |
---|
[c8e1996] | 1378 | state.from_xml(node=nodes[0]) |
---|
[2f4b430] | 1379 | |
---|
[61cada5] | 1380 | except: |
---|
[6c382da] | 1381 | logging.info("XML document does not contain fitting information.\n" |
---|
| 1382 | + traceback.format_exc()) |
---|
[2f4b430] | 1383 | |
---|
[61cada5] | 1384 | return state |
---|
[2f4b430] | 1385 | |
---|
[e89aed5] | 1386 | def _parse_simfit_state(self, entry): |
---|
| 1387 | """ |
---|
| 1388 | Parses the saved data for a simultaneous fit |
---|
| 1389 | :param entry: XML object to read from |
---|
| 1390 | :return: XML object for a simultaneous fit or None |
---|
| 1391 | """ |
---|
| 1392 | nodes = entry.xpath('ns:%s' % FITTING_NODE_NAME, |
---|
| 1393 | namespaces={'ns': CANSAS_NS}) |
---|
| 1394 | if nodes: |
---|
| 1395 | simfitstate = nodes[0].xpath('ns:simultaneous_fit', |
---|
| 1396 | namespaces={'ns': CANSAS_NS}) |
---|
| 1397 | if simfitstate: |
---|
| 1398 | from simfitpage import SimFitPageState |
---|
| 1399 | sim_fit_state = SimFitPageState() |
---|
| 1400 | simfitstate_0 = simfitstate[0] |
---|
| 1401 | all = simfitstate_0.xpath('ns:select_all', |
---|
[c8e1996] | 1402 | namespaces={'ns': CANSAS_NS}) |
---|
[e89aed5] | 1403 | atts = all[0].attrib |
---|
| 1404 | checked = atts.get('checked') |
---|
| 1405 | sim_fit_state.select_all = bool(checked) |
---|
| 1406 | model_list = simfitstate_0.xpath('ns:model_list', |
---|
[c8e1996] | 1407 | namespaces={'ns': CANSAS_NS}) |
---|
[e89aed5] | 1408 | model_list_items = model_list[0].xpath('ns:model_list_item', |
---|
[c8e1996] | 1409 | namespaces={'ns': |
---|
| 1410 | CANSAS_NS}) |
---|
[e89aed5] | 1411 | for model in model_list_items: |
---|
| 1412 | attrs = model.attrib |
---|
| 1413 | sim_fit_state.model_list.append(attrs) |
---|
[998ca90] | 1414 | |
---|
[e89aed5] | 1415 | constraints = simfitstate_0.xpath('ns:constraints', |
---|
| 1416 | namespaces={'ns': CANSAS_NS}) |
---|
| 1417 | constraint_list = constraints[0].xpath('ns:constraint', |
---|
[998ca90] | 1418 | namespaces={'ns': CANSAS_NS}) |
---|
[e89aed5] | 1419 | for constraint in constraint_list: |
---|
| 1420 | attrs = constraint.attrib |
---|
| 1421 | sim_fit_state.constraints_list.append(attrs) |
---|
| 1422 | |
---|
| 1423 | return sim_fit_state |
---|
| 1424 | else: |
---|
| 1425 | return None |
---|
| 1426 | |
---|
[ac5b69d] | 1427 | def _parse_save_state_entry(self, dom): |
---|
[e9b12eaf] | 1428 | """ |
---|
[5062bbf] | 1429 | Parse a SASentry |
---|
[2f4b430] | 1430 | |
---|
[5062bbf] | 1431 | :param node: SASentry node |
---|
[2f4b430] | 1432 | |
---|
[df7ed14] | 1433 | :return: Data1D/Data2D object |
---|
[2f4b430] | 1434 | |
---|
[e9b12eaf] | 1435 | """ |
---|
[df7ed14] | 1436 | node = dom.xpath('ns:data_class', namespaces={'ns': CANSAS_NS}) |
---|
| 1437 | if not node or node[0].text.lstrip().rstrip() != "Data2D": |
---|
[ac5b69d] | 1438 | return_value, _ = self._parse_entry(dom) |
---|
| 1439 | numpy.trim_zeros(return_value.x) |
---|
| 1440 | numpy.trim_zeros(return_value.y) |
---|
| 1441 | numpy.trim_zeros(return_value.dy) |
---|
| 1442 | size_dx = return_value.dx.size |
---|
| 1443 | size_dxl = return_value.dxl.size |
---|
| 1444 | size_dxw = return_value.dxw.size |
---|
| 1445 | if size_dxl == 0 and size_dxw == 0: |
---|
| 1446 | return_value.dxl = None |
---|
| 1447 | return_value.dxw = None |
---|
| 1448 | numpy.trim_zeros(return_value.dx) |
---|
| 1449 | elif size_dx == 0: |
---|
| 1450 | return_value.dx = None |
---|
| 1451 | size_dx = size_dxl |
---|
| 1452 | numpy.trim_zeros(return_value.dxl) |
---|
| 1453 | numpy.trim_zeros(return_value.dxw) |
---|
[2f4b430] | 1454 | |
---|
[ac5b69d] | 1455 | return return_value, _ |
---|
[2f4b430] | 1456 | |
---|
[c8e1996] | 1457 | # Parse 2D |
---|
[e9b12eaf] | 1458 | data_info = Data2D() |
---|
[2f4b430] | 1459 | |
---|
[f32d144] | 1460 | # Look up title |
---|
[e9b12eaf] | 1461 | self._store_content('ns:Title', dom, 'title', data_info) |
---|
[2f4b430] | 1462 | |
---|
[f32d144] | 1463 | # Look up run number |
---|
[e9b12eaf] | 1464 | nodes = dom.xpath('ns:Run', namespaces={'ns': CANSAS_NS}) |
---|
[f32d144] | 1465 | for item in nodes: |
---|
[e9b12eaf] | 1466 | if item.text is not None: |
---|
| 1467 | value = item.text.strip() |
---|
| 1468 | if len(value) > 0: |
---|
| 1469 | data_info.run.append(value) |
---|
| 1470 | if item.get('name') is not None: |
---|
| 1471 | data_info.run_name[value] = item.get('name') |
---|
[2f4b430] | 1472 | |
---|
[f32d144] | 1473 | # Look up instrument name |
---|
| 1474 | self._store_content('ns:SASinstrument/ns:name', dom, |
---|
| 1475 | 'instrument', data_info) |
---|
[e9b12eaf] | 1476 | |
---|
| 1477 | # Notes |
---|
| 1478 | note_list = dom.xpath('ns:SASnote', namespaces={'ns': CANSAS_NS}) |
---|
| 1479 | for note in note_list: |
---|
| 1480 | try: |
---|
| 1481 | if note.text is not None: |
---|
| 1482 | note_value = note.text.strip() |
---|
| 1483 | if len(note_value) > 0: |
---|
| 1484 | data_info.notes.append(note_value) |
---|
[7673ecd] | 1485 | except Exception: |
---|
[998ca90] | 1486 | err_mess = "cansas_reader.read: error processing entry notes\n" |
---|
| 1487 | err_mess += " %s" % sys.exc_value |
---|
[e9b12eaf] | 1488 | self.errors.append(err_mess) |
---|
| 1489 | logging.error(err_mess) |
---|
[2f4b430] | 1490 | |
---|
[e9b12eaf] | 1491 | # Sample info ################### |
---|
| 1492 | entry = get_content('ns:SASsample', dom) |
---|
| 1493 | if entry is not None: |
---|
| 1494 | data_info.sample.name = entry.get('name') |
---|
[2f4b430] | 1495 | |
---|
[b1e609c] | 1496 | self._store_content('ns:SASsample/ns:ID', dom, 'ID', data_info.sample) |
---|
[998ca90] | 1497 | self._store_float('ns:SASsample/ns:thickness', dom, 'thickness', |
---|
| 1498 | data_info.sample) |
---|
| 1499 | self._store_float('ns:SASsample/ns:transmission', dom, 'transmission', |
---|
| 1500 | data_info.sample) |
---|
| 1501 | self._store_float('ns:SASsample/ns:temperature', dom, 'temperature', |
---|
| 1502 | data_info.sample) |
---|
| 1503 | |
---|
| 1504 | nodes = dom.xpath('ns:SASsample/ns:details', |
---|
| 1505 | namespaces={'ns': CANSAS_NS}) |
---|
[e9b12eaf] | 1506 | for item in nodes: |
---|
| 1507 | try: |
---|
| 1508 | if item.text is not None: |
---|
| 1509 | detail_value = item.text.strip() |
---|
| 1510 | if len(detail_value) > 0: |
---|
| 1511 | data_info.sample.details.append(detail_value) |
---|
[7673ecd] | 1512 | except Exception: |
---|
[998ca90] | 1513 | err_mess = "cansas_reader.read: error processing entry notes\n" |
---|
| 1514 | err_mess += " %s" % sys.exc_value |
---|
[e9b12eaf] | 1515 | self.errors.append(err_mess) |
---|
| 1516 | logging.error(err_mess) |
---|
[2f4b430] | 1517 | |
---|
[e9b12eaf] | 1518 | # Position (as a vector) |
---|
[998ca90] | 1519 | self._store_float('ns:SASsample/ns:position/ns:x', dom, 'position.x', |
---|
| 1520 | data_info.sample) |
---|
| 1521 | self._store_float('ns:SASsample/ns:position/ns:y', dom, 'position.y', |
---|
| 1522 | data_info.sample) |
---|
| 1523 | self._store_float('ns:SASsample/ns:position/ns:z', dom, 'position.z', |
---|
| 1524 | data_info.sample) |
---|
[2f4b430] | 1525 | |
---|
[e9b12eaf] | 1526 | # Orientation (as a vector) |
---|
[f32d144] | 1527 | self._store_float('ns:SASsample/ns:orientation/ns:roll', |
---|
[b1e609c] | 1528 | dom, 'orientation.x', data_info.sample) |
---|
[f32d144] | 1529 | self._store_float('ns:SASsample/ns:orientation/ns:pitch', |
---|
[b1e609c] | 1530 | dom, 'orientation.y', data_info.sample) |
---|
[f32d144] | 1531 | self._store_float('ns:SASsample/ns:orientation/ns:yaw', |
---|
[b1e609c] | 1532 | dom, 'orientation.z', data_info.sample) |
---|
[2f4b430] | 1533 | |
---|
[e9b12eaf] | 1534 | # Source info ################### |
---|
| 1535 | entry = get_content('ns:SASinstrument/ns:SASsource', dom) |
---|
| 1536 | if entry is not None: |
---|
| 1537 | data_info.source.name = entry.get('name') |
---|
[2f4b430] | 1538 | |
---|
[f32d144] | 1539 | self._store_content('ns:SASinstrument/ns:SASsource/ns:radiation', |
---|
[b1e609c] | 1540 | dom, 'radiation', data_info.source) |
---|
[f32d144] | 1541 | self._store_content('ns:SASinstrument/ns:SASsource/ns:beam_shape', |
---|
[b1e609c] | 1542 | dom, 'beam_shape', data_info.source) |
---|
[f32d144] | 1543 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength', |
---|
[b1e609c] | 1544 | dom, 'wavelength', data_info.source) |
---|
[f32d144] | 1545 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_min', |
---|
[b1e609c] | 1546 | dom, 'wavelength_min', data_info.source) |
---|
[f32d144] | 1547 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_max', |
---|
[b1e609c] | 1548 | dom, 'wavelength_max', data_info.source) |
---|
[f32d144] | 1549 | self._store_float('ns:SASinstrument/ns:SASsource/ns:wavelength_spread', |
---|
[b1e609c] | 1550 | dom, 'wavelength_spread', data_info.source) |
---|
[2f4b430] | 1551 | |
---|
[f32d144] | 1552 | # Beam size (as a vector) |
---|
[e9b12eaf] | 1553 | entry = get_content('ns:SASinstrument/ns:SASsource/ns:beam_size', dom) |
---|
| 1554 | if entry is not None: |
---|
| 1555 | data_info.source.beam_size_name = entry.get('name') |
---|
[2f4b430] | 1556 | |
---|
[f32d144] | 1557 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:x', |
---|
[b1e609c] | 1558 | dom, 'beam_size.x', data_info.source) |
---|
[f32d144] | 1559 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:y', |
---|
[b1e609c] | 1560 | dom, 'beam_size.y', data_info.source) |
---|
[f32d144] | 1561 | self._store_float('ns:SASinstrument/ns:SASsource/ns:beam_size/ns:z', |
---|
[b1e609c] | 1562 | dom, 'beam_size.z', data_info.source) |
---|
[2f4b430] | 1563 | |
---|
[e9b12eaf] | 1564 | # Collimation info ################### |
---|
[f32d144] | 1565 | nodes = dom.xpath('ns:SASinstrument/ns:SAScollimation', |
---|
| 1566 | namespaces={'ns': CANSAS_NS}) |
---|
[e9b12eaf] | 1567 | for item in nodes: |
---|
| 1568 | collim = Collimation() |
---|
| 1569 | if item.get('name') is not None: |
---|
| 1570 | collim.name = item.get('name') |
---|
[f32d144] | 1571 | self._store_float('ns:length', item, 'length', collim) |
---|
[2f4b430] | 1572 | |
---|
[e9b12eaf] | 1573 | # Look for apertures |
---|
[f32d144] | 1574 | apert_list = item.xpath('ns:aperture', |
---|
| 1575 | namespaces={'ns': CANSAS_NS}) |
---|
[e9b12eaf] | 1576 | for apert in apert_list: |
---|
[f32d144] | 1577 | aperture = Aperture() |
---|
[2f4b430] | 1578 | |
---|
[e9b12eaf] | 1579 | # Get the name and type of the aperture |
---|
| 1580 | aperture.name = apert.get('name') |
---|
| 1581 | aperture.type = apert.get('type') |
---|
[2f4b430] | 1582 | |
---|
[f32d144] | 1583 | self._store_float('ns:distance', apert, 'distance', aperture) |
---|
[2f4b430] | 1584 | |
---|
[e9b12eaf] | 1585 | entry = get_content('ns:size', apert) |
---|
| 1586 | if entry is not None: |
---|
| 1587 | aperture.size_name = entry.get('name') |
---|
[2f4b430] | 1588 | |
---|
[f32d144] | 1589 | self._store_float('ns:size/ns:x', apert, 'size.x', aperture) |
---|
| 1590 | self._store_float('ns:size/ns:y', apert, 'size.y', aperture) |
---|
[e9b12eaf] | 1591 | self._store_float('ns:size/ns:z', apert, 'size.z', aperture) |
---|
[2f4b430] | 1592 | |
---|
[e9b12eaf] | 1593 | collim.aperture.append(aperture) |
---|
[2f4b430] | 1594 | |
---|
[e9b12eaf] | 1595 | data_info.collimation.append(collim) |
---|
[2f4b430] | 1596 | |
---|
[e9b12eaf] | 1597 | # Detector info ###################### |
---|
[f32d144] | 1598 | nodes = dom.xpath('ns:SASinstrument/ns:SASdetector', |
---|
| 1599 | namespaces={'ns': CANSAS_NS}) |
---|
[e9b12eaf] | 1600 | for item in nodes: |
---|
[2f4b430] | 1601 | |
---|
[e9b12eaf] | 1602 | detector = Detector() |
---|
[2f4b430] | 1603 | |
---|
[e9b12eaf] | 1604 | self._store_content('ns:name', item, 'name', detector) |
---|
[f32d144] | 1605 | self._store_float('ns:SDD', item, 'distance', detector) |
---|
[2f4b430] | 1606 | |
---|
[e9b12eaf] | 1607 | # Detector offset (as a vector) |
---|
[f32d144] | 1608 | self._store_float('ns:offset/ns:x', item, 'offset.x', detector) |
---|
| 1609 | self._store_float('ns:offset/ns:y', item, 'offset.y', detector) |
---|
| 1610 | self._store_float('ns:offset/ns:z', item, 'offset.z', detector) |
---|
[2f4b430] | 1611 | |
---|
[e9b12eaf] | 1612 | # Detector orientation (as a vector) |
---|
[f32d144] | 1613 | self._store_float('ns:orientation/ns:roll', item, |
---|
| 1614 | 'orientation.x', detector) |
---|
| 1615 | self._store_float('ns:orientation/ns:pitch', item, |
---|
| 1616 | 'orientation.y', detector) |
---|
| 1617 | self._store_float('ns:orientation/ns:yaw', item, |
---|
| 1618 | 'orientation.z', detector) |
---|
[2f4b430] | 1619 | |
---|
[e9b12eaf] | 1620 | # Beam center (as a vector) |
---|
[f32d144] | 1621 | self._store_float('ns:beam_center/ns:x', item, |
---|
| 1622 | 'beam_center.x', detector) |
---|
| 1623 | self._store_float('ns:beam_center/ns:y', item, |
---|
| 1624 | 'beam_center.y', detector) |
---|
| 1625 | self._store_float('ns:beam_center/ns:z', item, |
---|
| 1626 | 'beam_center.z', detector) |
---|
[2f4b430] | 1627 | |
---|
[e9b12eaf] | 1628 | # Pixel size (as a vector) |
---|
[f32d144] | 1629 | self._store_float('ns:pixel_size/ns:x', item, |
---|
| 1630 | 'pixel_size.x', detector) |
---|
| 1631 | self._store_float('ns:pixel_size/ns:y', item, |
---|
| 1632 | 'pixel_size.y', detector) |
---|
| 1633 | self._store_float('ns:pixel_size/ns:z', item, |
---|
| 1634 | 'pixel_size.z', detector) |
---|
[2f4b430] | 1635 | |
---|
[e9b12eaf] | 1636 | self._store_float('ns:slit_length', item, 'slit_length', detector) |
---|
[2f4b430] | 1637 | |
---|
[f32d144] | 1638 | data_info.detector.append(detector) |
---|
[e9b12eaf] | 1639 | |
---|
| 1640 | # Processes info ###################### |
---|
| 1641 | nodes = dom.xpath('ns:SASprocess', namespaces={'ns': CANSAS_NS}) |
---|
| 1642 | for item in nodes: |
---|
| 1643 | process = Process() |
---|
| 1644 | self._store_content('ns:name', item, 'name', process) |
---|
| 1645 | self._store_content('ns:date', item, 'date', process) |
---|
| 1646 | self._store_content('ns:description', item, 'description', process) |
---|
[2f4b430] | 1647 | |
---|
[e9b12eaf] | 1648 | term_list = item.xpath('ns:term', namespaces={'ns': CANSAS_NS}) |
---|
| 1649 | for term in term_list: |
---|
| 1650 | try: |
---|
| 1651 | term_attr = {} |
---|
| 1652 | for attr in term.keys(): |
---|
| 1653 | term_attr[attr] = term.get(attr).strip() |
---|
| 1654 | if term.text is not None: |
---|
| 1655 | term_attr['value'] = term.text.strip() |
---|
| 1656 | process.term.append(term_attr) |
---|
| 1657 | except: |
---|
[998ca90] | 1658 | err_mess = "cansas_reader.read: error processing " |
---|
| 1659 | err_mess += "entry notes\n %s" % sys.exc_value |
---|
[e9b12eaf] | 1660 | self.errors.append(err_mess) |
---|
| 1661 | logging.error(err_mess) |
---|
[2f4b430] | 1662 | |
---|
[f32d144] | 1663 | note_list = item.xpath('ns:SASprocessnote', |
---|
| 1664 | namespaces={'ns': CANSAS_NS}) |
---|
[e9b12eaf] | 1665 | for note in note_list: |
---|
| 1666 | if note.text is not None: |
---|
| 1667 | process.notes.append(note.text.strip()) |
---|
[2f4b430] | 1668 | |
---|
[e9b12eaf] | 1669 | data_info.process.append(process) |
---|
[2f4b430] | 1670 | |
---|
[e9b12eaf] | 1671 | # Data info ###################### |
---|
| 1672 | nodes = dom.xpath('ns:SASdata', namespaces={'ns': CANSAS_NS}) |
---|
[f32d144] | 1673 | if len(nodes) > 1: |
---|
[a95ae9a] | 1674 | raise RuntimeError, "CanSAS reader is not compatible with" + \ |
---|
| 1675 | " multiple SASdata entries" |
---|
[2f4b430] | 1676 | |
---|
[df7ed14] | 1677 | for entry in nodes: |
---|
[b1e609c] | 1678 | for item in LIST_OF_DATA_2D_ATTR: |
---|
[c8e1996] | 1679 | # get node |
---|
[f32d144] | 1680 | node = get_content('ns:%s' % item[0], entry) |
---|
[b1e609c] | 1681 | setattr(data_info, item[1], parse_entry_helper(node, item)) |
---|
[2f4b430] | 1682 | |
---|
[b1e609c] | 1683 | for item in LIST_OF_DATA_2D_VALUES: |
---|
[f32d144] | 1684 | field = get_content('ns:%s' % item[0], entry) |
---|
[b1e609c] | 1685 | value_list = [] |
---|
[df7ed14] | 1686 | if field is not None: |
---|
[998ca90] | 1687 | value_list = \ |
---|
| 1688 | [parse_entry_helper(node, item) for node in field] |
---|
[b1e609c] | 1689 | if len(value_list) < 2: |
---|
| 1690 | setattr(data_info, item[0], None) |
---|
[44f7c1b] | 1691 | else: |
---|
[b1e609c] | 1692 | setattr(data_info, item[0], numpy.array(value_list)) |
---|
[2f4b430] | 1693 | |
---|
[e9b12eaf] | 1694 | return data_info |
---|
| 1695 | |
---|
[61cada5] | 1696 | def _read_cansas(self, path): |
---|
[f32d144] | 1697 | """ |
---|
[e89aed5] | 1698 | Load data and fitting information from a CanSAS XML file. |
---|
[2f4b430] | 1699 | |
---|
[5062bbf] | 1700 | :param path: file path |
---|
[f32d144] | 1701 | :return: Data1D object if a single SASentry was found, |
---|
[5062bbf] | 1702 | or a list of Data1D objects if multiple entries were found, |
---|
| 1703 | or None of nothing was found |
---|
| 1704 | :raise RuntimeError: when the file can't be opened |
---|
| 1705 | :raise ValueError: when the length of the data vectors are inconsistent |
---|
[61cada5] | 1706 | """ |
---|
| 1707 | output = [] |
---|
[e89aed5] | 1708 | simfitstate = None |
---|
[f32d144] | 1709 | basename = os.path.basename(path) |
---|
[b63dc6e] | 1710 | root, extension = os.path.splitext(basename) |
---|
| 1711 | ext = extension.lower() |
---|
[61cada5] | 1712 | try: |
---|
| 1713 | if os.path.isfile(path): |
---|
[a95ae9a] | 1714 | if ext in self.ext or ext == '.xml': |
---|
[61cada5] | 1715 | tree = etree.parse(path, parser=etree.ETCompatXMLParser()) |
---|
| 1716 | # Check the format version number |
---|
[a95ae9a] | 1717 | # Specifying the namespace will take care of the file |
---|
| 1718 | # format version |
---|
[61cada5] | 1719 | root = tree.getroot() |
---|
[f32d144] | 1720 | entry_list = root.xpath('ns:SASentry', |
---|
| 1721 | namespaces={'ns': CANSAS_NS}) |
---|
| 1722 | for entry in entry_list: |
---|
[e9b12eaf] | 1723 | try: |
---|
[ac5b69d] | 1724 | sas_entry, _ = self._parse_save_state_entry(entry) |
---|
[e9b12eaf] | 1725 | except: |
---|
[df7ed14] | 1726 | raise |
---|
[61cada5] | 1727 | fitstate = self._parse_state(entry) |
---|
[2f4b430] | 1728 | |
---|
[a95ae9a] | 1729 | # state could be None when .svs file is loaded |
---|
| 1730 | # in this case, skip appending to output |
---|
| 1731 | if fitstate is not None: |
---|
[b35d3d1] | 1732 | sas_entry.meta_data['fitstate'] = fitstate |
---|
| 1733 | sas_entry.filename = fitstate.file |
---|
| 1734 | output.append(sas_entry) |
---|
[e89aed5] | 1735 | |
---|
[61cada5] | 1736 | else: |
---|
[b63dc6e] | 1737 | self.call_back(format=ext) |
---|
[61cada5] | 1738 | raise RuntimeError, "%s is not a file" % path |
---|
[b35d3d1] | 1739 | |
---|
[61cada5] | 1740 | # Return output consistent with the loader's api |
---|
[f32d144] | 1741 | if len(output) == 0: |
---|
| 1742 | self.call_back(state=None, datainfo=None, format=ext) |
---|
[61cada5] | 1743 | return None |
---|
| 1744 | else: |
---|
[b35d3d1] | 1745 | for ind in range(len(output)): |
---|
| 1746 | # Call back to post the new state |
---|
| 1747 | state = output[ind].meta_data['fitstate'] |
---|
| 1748 | t = time.localtime(state.timestamp) |
---|
| 1749 | time_str = time.strftime("%b %d %H:%M", t) |
---|
| 1750 | # Check that no time stamp is already appended |
---|
| 1751 | max_char = state.file.find("[") |
---|
| 1752 | if max_char < 0: |
---|
| 1753 | max_char = len(state.file) |
---|
[ef16f59] | 1754 | original_fname = state.file[0:max_char] |
---|
[f32d144] | 1755 | state.file = original_fname + ' [' + time_str + ']' |
---|
[2f4b430] | 1756 | |
---|
[b35d3d1] | 1757 | if state is not None and state.is_data is not None: |
---|
[b1e609c] | 1758 | output[ind].is_data = state.is_data |
---|
[2f4b430] | 1759 | |
---|
[b35d3d1] | 1760 | output[ind].filename = state.file |
---|
| 1761 | state.data = output[ind] |
---|
[f32d144] | 1762 | state.data.name = output[ind].filename # state.data_name |
---|
[b35d3d1] | 1763 | state.data.id = state.data_id |
---|
| 1764 | if state.is_data is not None: |
---|
| 1765 | state.data.is_data = state.is_data |
---|
[f32d144] | 1766 | if output[ind].run_name is not None\ |
---|
[c8e1996] | 1767 | and len(output[ind].run_name) != 0: |
---|
[654e8e0] | 1768 | if isinstance(output[ind].run_name, dict): |
---|
| 1769 | name = output[ind].run_name.keys()[0] |
---|
| 1770 | else: |
---|
| 1771 | name = output[ind].run_name |
---|
[f32d144] | 1772 | else: |
---|
| 1773 | name = original_fname |
---|
[ef16f59] | 1774 | state.data.group_id = name |
---|
[a95ae9a] | 1775 | # store state in fitting |
---|
[f32d144] | 1776 | self.call_back(state=state, |
---|
| 1777 | datainfo=output[ind], format=ext) |
---|
| 1778 | self.state = state |
---|
[e6de6b8] | 1779 | simfitstate = self._parse_simfit_state(entry) |
---|
[e89aed5] | 1780 | if simfitstate is not None: |
---|
| 1781 | self.call_back(state=simfitstate) |
---|
| 1782 | |
---|
[ef16f59] | 1783 | return output |
---|
[61cada5] | 1784 | except: |
---|
[4bee68d] | 1785 | self.call_back(format=ext) |
---|
[61cada5] | 1786 | raise |
---|
[2f4b430] | 1787 | |
---|
[61cada5] | 1788 | def write(self, filename, datainfo=None, fitstate=None): |
---|
| 1789 | """ |
---|
[b35d3d1] | 1790 | Write the content of a Data1D as a CanSAS XML file only for standalone |
---|
[2f4b430] | 1791 | |
---|
[5062bbf] | 1792 | :param filename: name of the file to write |
---|
| 1793 | :param datainfo: Data1D object |
---|
| 1794 | :param fitstate: PageState object |
---|
[2f4b430] | 1795 | |
---|
[61cada5] | 1796 | """ |
---|
| 1797 | # Sanity check |
---|
[a95ae9a] | 1798 | if self.cansas: |
---|
[61cada5] | 1799 | # Add fitting information to the XML document |
---|
[ef16f59] | 1800 | doc = self.write_toXML(datainfo, fitstate) |
---|
[61cada5] | 1801 | # Write the XML document |
---|
| 1802 | else: |
---|
[c8e1996] | 1803 | doc = fitstate.to_xml(file=filename) |
---|
[2f4b430] | 1804 | |
---|
[ac5b69d] | 1805 | # Save the document no matter the type |
---|
| 1806 | fd = open(filename, 'w') |
---|
| 1807 | fd.write(doc.toprettyxml()) |
---|
| 1808 | fd.close() |
---|
[2f4b430] | 1809 | |
---|
[a95ae9a] | 1810 | def write_toXML(self, datainfo=None, state=None, batchfit=None): |
---|
[b35d3d1] | 1811 | """ |
---|
[f32d144] | 1812 | Write toXML, a helper for write(), |
---|
| 1813 | could be used by guimanager._on_save() |
---|
[2f4b430] | 1814 | |
---|
[b35d3d1] | 1815 | : return: xml doc |
---|
| 1816 | """ |
---|
[3c44c66] | 1817 | |
---|
[a95ae9a] | 1818 | self.batchfit_params = batchfit |
---|
| 1819 | if state.data is None or not state.data.is_data: |
---|
[3b148c3] | 1820 | return None |
---|
[a95ae9a] | 1821 | # make sure title and data run are filled. |
---|
| 1822 | if state.data.title is None or state.data.title == '': |
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| 1823 | state.data.title = state.data.name |
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| 1824 | if state.data.run_name is None or state.data.run_name == {}: |
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| 1825 | state.data.run = [str(state.data.name)] |
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| 1826 | state.data.run_name[0] = state.data.name |
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| 1827 | |
---|
| 1828 | if issubclass(state.data.__class__, |
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| 1829 | sas.sascalc.dataloader.data_info.Data1D): |
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| 1830 | data = state.data |
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| 1831 | doc, sasentry = self._to_xml_doc(data) |
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[f32d144] | 1832 | else: |
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[a95ae9a] | 1833 | data = state.data |
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| 1834 | doc, sasentry = self._data2d_to_xml_doc(data) |
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[2f4b430] | 1835 | |
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[b35d3d1] | 1836 | if state is not None: |
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[c8e1996] | 1837 | doc = state.to_xml(doc=doc, file=data.filename, entry_node=sasentry, |
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| 1838 | batch_fit_state=self.batchfit_params) |
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[2f4b430] | 1839 | |
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[f32d144] | 1840 | return doc |
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[467202f] | 1841 | |
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| 1842 | # Simple html report templet |
---|
| 1843 | HEADER = "<html>\n" |
---|
| 1844 | HEADER += "<head>\n" |
---|
| 1845 | HEADER += "<meta http-equiv=Content-Type content='text/html; " |
---|
| 1846 | HEADER += "charset=windows-1252'> \n" |
---|
| 1847 | HEADER += "<meta name=Generator >\n" |
---|
| 1848 | HEADER += "</head>\n" |
---|
| 1849 | HEADER += "<body lang=EN-US>\n" |
---|
| 1850 | HEADER += "<div class=WordSection1>\n" |
---|
| 1851 | HEADER += "<p class=MsoNormal><b><span ><center><font size='4' >" |
---|
| 1852 | HEADER += "%s</font></center></span></center></b></p>" |
---|
| 1853 | HEADER += "<p class=MsoNormal> </p>" |
---|
| 1854 | PARA = "<p class=MsoNormal><font size='4' > %s \n" |
---|
| 1855 | PARA += "</font></p>" |
---|
| 1856 | CENTRE = "<p class=MsoNormal><center><font size='4' > %s \n" |
---|
| 1857 | CENTRE += "</font></center></p>" |
---|
| 1858 | FEET_1 = \ |
---|
| 1859 | """ |
---|
| 1860 | <p class=MsoNormal> </p> |
---|
| 1861 | <br> |
---|
| 1862 | <p class=MsoNormal><b><span ><center> <font size='4' > Graph |
---|
| 1863 | </font></span></center></b></p> |
---|
| 1864 | <p class=MsoNormal> </p> |
---|
| 1865 | <center> |
---|
| 1866 | <br><font size='4' >Model Computation</font> |
---|
| 1867 | <br><font size='4' >Data: "%s"</font><br> |
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| 1868 | """ |
---|
| 1869 | FEET_2 = \ |
---|
| 1870 | """ |
---|
| 1871 | <img src="%s" > |
---|
| 1872 | </img> |
---|
| 1873 | """ |
---|
| 1874 | FEET_3 = \ |
---|
| 1875 | """ |
---|
| 1876 | </center> |
---|
| 1877 | </div> |
---|
| 1878 | </body> |
---|
| 1879 | </html> |
---|
| 1880 | """ |
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[c8e1996] | 1881 | ELINE = "<p class=MsoNormal> </p>" |
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