[e02d8f6] | 1 | import time |
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| 2 | import sys |
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| 3 | import os |
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| 4 | import sas.sascalc.dataloader |
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| 5 | from lxml import etree |
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| 6 | from sas.sascalc.dataloader.readers.cansas_reader import Reader as CansasReader |
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| 7 | from sas.sascalc.dataloader.readers.cansas_reader import get_content |
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| 8 | from sas.sasgui.guiframe.utils import format_number |
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| 9 | from sas.sasgui.guiframe.gui_style import GUIFRAME_ID |
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| 10 | from sas.sasgui.guiframe.dataFitting import Data1D |
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| 11 | from sas.sascalc.dataloader.loader import Loader |
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| 12 | |
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| 13 | CORNODE_NAME = 'corfunc' |
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| 14 | CANSAS_NS = 'cansas1d/1.0' |
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| 15 | |
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| 16 | # The default state |
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| 17 | DEFAULT_STATE = { |
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| 18 | 'qmin_tcl': None, |
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| 19 | 'qmax1_tcl': None, |
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| 20 | 'qmax2_tcl': None, |
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[b564ea2] | 21 | 'background_tcl': None |
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[e02d8f6] | 22 | } |
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| 23 | |
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| 24 | # List of output parameters, used by __str__ |
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| 25 | output_list = [ |
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| 26 | ["long_period", "Long Period"], |
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| 27 | ["hard_block_thickness", "Average Hard Block Thickness"], |
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| 28 | ["interface_thickness", "Average Interface Thickness"], |
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| 29 | ["core_thickness", "Average Core Thickness"], |
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| 30 | ["polydispersity", "PolyDispersity"], |
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| 31 | ["filling", "Filling Fraction"] |
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| 32 | ] |
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| 33 | |
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| 34 | class CorfuncState(object): |
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[9c90cf3] | 35 | """ |
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| 36 | Stores information about the state of CorfuncPanel |
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| 37 | """ |
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[e02d8f6] | 38 | |
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| 39 | def __init__(self): |
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| 40 | # Inputs |
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| 41 | self.file = None |
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| 42 | self.data = None |
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| 43 | self.qmin = None |
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| 44 | self.qmax = [0, 0] |
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[b564ea2] | 45 | self.background = None |
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[e02d8f6] | 46 | self.outputs = None |
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| 47 | |
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| 48 | self.saved_state = DEFAULT_STATE |
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| 49 | # Will be filled on panel init as number of states increases |
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| 50 | self.state_list = {} |
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| 51 | self.timestamp = time.time() |
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| 52 | |
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| 53 | # Raw Data |
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| 54 | self.q = None |
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| 55 | self.iq = None |
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| 56 | # TODO: Add extrapolated data and transformed data (when implemented) |
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| 57 | |
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| 58 | def __str__(self): |
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| 59 | """ |
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| 60 | Pretty print the state |
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| 61 | |
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| 62 | :return: A string representing the state |
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| 63 | """ |
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| 64 | state = "File: {}\n".format(self.file) |
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| 65 | state += "Timestamp: {}\n".format(self.timestamp) |
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| 66 | state += "Qmin: {}\n".format(str(self.qmin)) |
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| 67 | state += "Qmax: {}\n".format(str(self.qmax)) |
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[b564ea2] | 68 | state += "Background: {}\n".format(str(self.background)) |
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[e02d8f6] | 69 | if self.outputs is None: |
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| 70 | return state |
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| 71 | state += "\nOutputs:\n" |
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| 72 | for output in output_list: |
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| 73 | key = output[0] |
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| 74 | name = output[1] |
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| 75 | state += "{}: {}\n".format(name, str(self.outputs[key])) |
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| 76 | |
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| 77 | return state |
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| 78 | |
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| 79 | def set_saved_state(self, name, value): |
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| 80 | """ |
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| 81 | Set a value in the current state. |
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| 82 | |
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| 83 | :param name: The name of the parameter to set |
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| 84 | :param value: The value to set the parameter to |
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| 85 | """ |
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| 86 | self.saved_state[name] = value |
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| 87 | if name == 'qmin_tcl': |
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| 88 | self.qmin = value |
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| 89 | elif name == 'qmax1_tcl': |
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| 90 | self.qmax[0] = value |
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| 91 | elif name == 'qmax2_tcl': |
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| 92 | self.qmax[1] = value |
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[b564ea2] | 93 | elif name == 'background_tcl': |
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| 94 | self.background = value |
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[e02d8f6] | 95 | |
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| 96 | def toXML(self, filename='corfunc_state.cor', doc=None, entry_node=None): |
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| 97 | """ |
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| 98 | Writes the state of the CorfuncPanel panel to file, as XML. |
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| 99 | |
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| 100 | Compatible with standalone writing, or appending to an |
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| 101 | already existing XML document. In that case, the XML document |
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| 102 | is required. An optional entry node in the XML document |
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| 103 | may also be given. |
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| 104 | |
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| 105 | :param file: file to write to |
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| 106 | :param doc: XML document object [optional] |
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| 107 | :param entry_node: XML node within the XML document at which |
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| 108 | we will append the data [optional] |
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| 109 | |
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[77e9ac6] | 110 | :return: None if no doc is provided, modified XML document if doc!=None |
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[e02d8f6] | 111 | """ |
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| 112 | from xml.dom.minidom import getDOMImplementation |
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| 113 | |
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| 114 | top_element = None |
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| 115 | new_doc = None |
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| 116 | if doc is None: |
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| 117 | # Create a new XML document |
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| 118 | impl = getDOMImplementation() |
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| 119 | doc_type = impl.createDocumentType(CORNODE_NAME, "1.0", "1.0") |
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| 120 | new_doc = impl.createDocument(None, CORNODE_NAME, doc_type) |
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| 121 | top_element = new_doc.documentElement |
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| 122 | else: |
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| 123 | # Create a new element in the document provided |
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| 124 | top_element = doc.createElement(CORNODE_NAME) |
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| 125 | if entry_node is None: |
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| 126 | doc.documentElement.appendChild(top_element) |
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| 127 | else: |
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| 128 | entry_node.appendChild(top_element) |
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| 129 | new_doc = doc |
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| 130 | |
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| 131 | # Version |
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| 132 | attr = new_doc.createAttribute("version") |
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| 133 | attr.nodeValue = '1.0' |
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| 134 | top_element.setAttributeNode(attr) |
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| 135 | |
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| 136 | # Filename |
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| 137 | element = new_doc.createElement("filename") |
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| 138 | if self.file is not None and self.file != '': |
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| 139 | element.appendChild(new_doc.createTextNode(str(self.file))) |
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| 140 | else: |
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| 141 | element.appendChild(new_doc.createTextNode(str(filename))) |
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| 142 | top_element.appendChild(element) |
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| 143 | |
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| 144 | # Timestamp |
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| 145 | element = new_doc.createElement("timestamp") |
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| 146 | # Pretty printed format |
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| 147 | element.appendChild(new_doc.createTextNode(time.ctime(self.timestamp))) |
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| 148 | attr = new_doc.createAttribute("epoch") |
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| 149 | # Epoch value (used in self.fromXML) |
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| 150 | attr.nodeValue = str(self.timestamp) |
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| 151 | element.setAttributeNode(attr) |
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| 152 | top_element.appendChild(element) |
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| 153 | |
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| 154 | # Current state |
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| 155 | state = new_doc.createElement("state") |
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| 156 | top_element.appendChild(state) |
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| 157 | for name, value in self.saved_state.iteritems(): |
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| 158 | element = new_doc.createElement(name) |
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| 159 | element.appendChild(new_doc.createTextNode(str(value))) |
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| 160 | state.appendChild(element) |
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| 161 | |
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| 162 | |
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| 163 | # Save the file or return the original document with the state |
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| 164 | # data appended |
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| 165 | if doc is None: |
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| 166 | fd = open(filename, 'w') |
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| 167 | fd.write(new_doc.toprettyxml()) |
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| 168 | fd.close() |
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| 169 | return None |
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| 170 | else: |
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| 171 | return new_doc |
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| 172 | |
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| 173 | |
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| 174 | def fromXML(self, node): |
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| 175 | """ |
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| 176 | Load corfunc states from a file |
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| 177 | |
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| 178 | :param node: node of an XML document to read from (optional) |
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| 179 | """ |
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| 180 | if node.get('version') and node.get('version') == '1.0': |
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| 181 | # Parse filename |
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| 182 | entry = get_content('ns:filename', node) |
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| 183 | if entry is not None: |
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| 184 | self.file = entry.text.strip() |
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| 185 | |
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| 186 | # Parse timestamp |
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| 187 | entry = get_content('ns:timestamp', node) |
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| 188 | if entry is not None and entry.get('epoch'): |
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| 189 | try: |
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| 190 | self.timestamp = (entry.get('epoch')) |
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| 191 | except: |
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| 192 | msg = ("CorfuncState.fromXML: Could not read timestamp", |
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| 193 | "\n{}").format(sys.exc_value) |
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| 194 | logging.error(msg) |
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| 195 | |
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| 196 | # Parse current state |
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| 197 | entry = get_content('ns:state', node) |
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| 198 | if entry is not None: |
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| 199 | for item in DEFAULT_STATE.iterkeys(): |
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| 200 | input_field = get_content("ns:{}".format(item), entry) |
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| 201 | if input_field is not None: |
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| 202 | try: |
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| 203 | value = float(input_field.text.strip()) |
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| 204 | except: |
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| 205 | value = None |
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| 206 | self.set_saved_state(name=item, value=value) |
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| 207 | |
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| 208 | |
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| 209 | |
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| 210 | class Reader(CansasReader): |
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| 211 | """ |
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[9c90cf3] | 212 | Reads a CanSAS file containing the state of a CorfuncPanel |
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[e02d8f6] | 213 | """ |
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| 214 | |
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| 215 | type_name = "Corfunc" |
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| 216 | |
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| 217 | def __init__(self, callback): |
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| 218 | self.callback = callback |
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| 219 | self.state = None |
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| 220 | |
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| 221 | def read(self, path): |
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| 222 | """ |
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| 223 | Load data and corfunc information frmo a CanSAS file. |
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| 224 | |
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| 225 | :param path: The file path to read from |
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| 226 | :return: Data1D object, a list of Data1D objects, or None |
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| 227 | :raise IOError: When the file can't be found |
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| 228 | :raise IOError: When the file is an invalid file type |
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| 229 | :raise ValueError: When the length of the data vectors are inconsistent |
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| 230 | """ |
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| 231 | output = [] |
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| 232 | if os.path.isfile(path): |
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| 233 | # Load file |
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| 234 | basename = os.path.basename(path) |
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| 235 | root, ext = os.path.splitext(basename) |
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| 236 | if ext.lower() != '.xml' and ext.lower() != '.svs': |
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| 237 | raise IOError, "{} is not a supported file type".format(ext) |
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| 238 | tree = etree.parse(path, parser=etree.ETCompatXMLParser()) |
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| 239 | root = tree.getroot() |
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| 240 | entry_list = root.xpath('/ns:SASroot/ns:SASentry', |
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| 241 | namespaces={'ns': CANSAS_NS}) |
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| 242 | for entry in entry_list: |
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| 243 | sas_entry, _ = self._parse_entry(entry) |
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| 244 | corstate = self._parse_state(entry) |
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| 245 | |
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| 246 | if corstate != None: |
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| 247 | sas_entry.meta_data['corstate'] = corstate |
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| 248 | sas_entry.filename = corstate.file |
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| 249 | output.append(sas_entry) |
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| 250 | else: |
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| 251 | # File not found |
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| 252 | msg = "{} is not a valid file path or doesn't exist".format(path) |
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| 253 | raise IOError, msg |
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| 254 | |
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| 255 | if len(output) == 0: |
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| 256 | return None |
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| 257 | elif len(output) == 1: |
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| 258 | self.callback(output[0].meta_data['corstate'], datainfo=output[0]) |
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| 259 | return output[0] |
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| 260 | else: |
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| 261 | return output |
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| 262 | |
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| 263 | def write(self, filename, datainfo=None, state=None): |
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| 264 | """ |
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| 265 | Write the content of a Data1D as a CanSAS file. |
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| 266 | |
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| 267 | : param filename: Name of the file to write |
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| 268 | : param datainfo: Data1D object |
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| 269 | : param state: CorfuncState object |
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| 270 | """ |
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| 271 | # Prepare datainfo |
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| 272 | if datainfo is None: |
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| 273 | datainfo = Data1D(x=[], y=[]) |
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| 274 | elif not issubclass(datainfo.__class__, Data1D): |
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| 275 | msg = ("The CanSAS writer expects a Data1D instance. {} was ", |
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| 276 | "provided").format(datainfo.__class__.__name__) |
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| 277 | raise RuntimeError, msg |
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| 278 | if datainfo.title is None or datainfo.title == '': |
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| 279 | datainfo.title = datainfo.name |
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| 280 | if datainfo.run_name == None or datainfo.run_name == '': |
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| 281 | datainfo.run = [str(datainfo.name)] |
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| 282 | datainfo.run_name[0] = datainfo.name |
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| 283 | |
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| 284 | # Create the XMl doc |
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| 285 | doc, sasentry = self._to_xml_doc(datainfo) |
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| 286 | if state is not None: |
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| 287 | doc = state.toXML(doc=doc, entry_node=sasentry) |
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| 288 | |
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| 289 | # Write the XML doc to a file |
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| 290 | fd = open(filename, 'w') |
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| 291 | fd.write(doc.toprettyxml()) |
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| 292 | fd.close() |
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| 293 | |
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| 294 | def get_state(self): |
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| 295 | return self.state |
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| 296 | |
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| 297 | |
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| 298 | def _parse_state(self, entry): |
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| 299 | """ |
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| 300 | Read state data from an XML node |
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| 301 | |
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| 302 | :param entry: The XML node to read from |
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| 303 | :return: CorfuncState object |
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| 304 | """ |
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| 305 | state = None |
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| 306 | try: |
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| 307 | nodes = entry.xpath('ns:{}'.format(CORNODE_NAME), |
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| 308 | namespaces={'ns': CANSAS_NS}) |
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| 309 | if nodes != []: |
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| 310 | state = CorfuncState() |
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| 311 | state.fromXML(nodes[0]) |
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| 312 | except: |
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| 313 | msg = "XML document does not contain CorfuncState information\n{}" |
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| 314 | msg.format(sys.exc_value) |
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| 315 | logging.info(msg) |
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| 316 | return state |
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