| 1 | import time |
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| 2 | import sys |
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| 3 | import os |
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| 4 | import logging |
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| 5 | import sas.sascalc.dataloader |
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| 6 | from lxml import etree |
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| 7 | from sas.sascalc.dataloader.readers.cansas_reader import Reader as CansasReader |
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| 8 | from sas.sascalc.dataloader.readers.cansas_reader import get_content |
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| 9 | from sas.sasgui.guiframe.utils import format_number |
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| 10 | from sas.sasgui.guiframe.gui_style import GUIFRAME_ID |
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| 11 | from sas.sasgui.guiframe.dataFitting import Data1D |
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| 12 | from sas.sascalc.dataloader.loader import Loader |
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| 13 | |
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| 14 | CORNODE_NAME = 'corfunc' |
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| 15 | CANSAS_NS = 'cansas1d/1.0' |
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| 16 | |
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| 17 | # The default state |
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| 18 | DEFAULT_STATE = { |
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| 19 | 'qmin_tcl': None, |
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| 20 | 'qmax1_tcl': None, |
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| 21 | 'qmax2_tcl': None, |
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| 22 | 'background_tcl': None |
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| 23 | } |
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| 24 | |
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| 25 | # List of output parameters, used by __str__ |
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| 26 | output_list = [ |
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| 27 | ['max', "Long Period (A): "], |
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| 28 | ['Lc', "Average Hard Block Thickness (A): "], |
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| 29 | ['dtr', "Average Interface Thickness (A): "], |
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| 30 | ['d0', "Average Core Thickness: "], |
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| 31 | ['A', "PolyDispersity: "], |
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| 32 | ['fill', "Filling Fraction: "] |
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| 33 | ] |
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| 34 | |
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| 35 | class CorfuncState(object): |
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| 36 | """ |
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| 37 | Stores information about the state of CorfuncPanel |
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| 38 | """ |
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| 39 | |
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| 40 | def __init__(self): |
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| 41 | # Inputs |
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| 42 | self.file = None |
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| 43 | self.data = None |
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| 44 | self.qmin = None |
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| 45 | self.qmax = [0, 0] |
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| 46 | self.background = None |
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| 47 | self.outputs = {} |
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| 48 | self.is_extrapolated = False |
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| 49 | self.is_transformed = False |
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| 50 | |
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| 51 | self.saved_state = DEFAULT_STATE |
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| 52 | # Will be filled on panel init as number of states increases |
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| 53 | self.state_list = {} |
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| 54 | self.timestamp = time.time() |
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| 55 | |
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| 56 | # Raw Data |
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| 57 | self.q = None |
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| 58 | self.iq = None |
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| 59 | # TODO: Add extrapolated data and transformed data (when implemented) |
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| 60 | |
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| 61 | def __str__(self): |
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| 62 | """ |
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| 63 | Pretty print the state |
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| 64 | |
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| 65 | :return: A string representing the state |
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| 66 | """ |
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| 67 | state = "File: {}\n".format(self.file) |
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| 68 | state += "Timestamp: {}\n".format(self.timestamp) |
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| 69 | state += "Qmin: {}\n".format(str(self.qmin)) |
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| 70 | state += "Qmax: {}\n".format(str(self.qmax)) |
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| 71 | state += "Background: {}\n".format(str(self.background)) |
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| 72 | if self.outputs is None: |
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| 73 | return state |
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| 74 | state += "\nOutputs:\n" |
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| 75 | for output in output_list: |
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| 76 | key = output[0] |
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| 77 | name = output[1] |
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| 78 | state += "{}: {}\n".format(name, str(self.outputs[key])) |
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| 79 | |
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| 80 | return state |
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| 81 | |
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| 82 | def set_saved_state(self, name, value): |
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| 83 | """ |
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| 84 | Set a value in the current state. |
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| 85 | |
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| 86 | :param name: The name of the parameter to set |
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| 87 | :param value: The value to set the parameter to |
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| 88 | """ |
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| 89 | self.saved_state[name] = value |
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| 90 | if name == 'qmin_tcl': |
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| 91 | self.qmin = value |
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| 92 | elif name == 'qmax1_tcl': |
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| 93 | self.qmax[0] = value |
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| 94 | elif name == 'qmax2_tcl': |
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| 95 | self.qmax[1] = value |
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| 96 | elif name == 'background_tcl': |
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| 97 | self.background = value |
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| 98 | |
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| 99 | def toXML(self, filename='corfunc_state.cor', doc=None, entry_node=None): |
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| 100 | """ |
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| 101 | Writes the state of the CorfuncPanel panel to file, as XML. |
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| 102 | |
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| 103 | Compatible with standalone writing, or appending to an |
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| 104 | already existing XML document. In that case, the XML document |
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| 105 | is required. An optional entry node in the XML document |
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| 106 | may also be given. |
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| 107 | |
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| 108 | :param file: file to write to |
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| 109 | :param doc: XML document object [optional] |
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| 110 | :param entry_node: XML node within the XML document at which |
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| 111 | we will append the data [optional] |
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| 112 | |
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| 113 | :return: None if no doc is provided, modified XML document if doc!=None |
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| 114 | """ |
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| 115 | from xml.dom.minidom import getDOMImplementation |
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| 116 | |
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| 117 | top_element = None |
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| 118 | new_doc = None |
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| 119 | if doc is None: |
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| 120 | # Create a new XML document |
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| 121 | impl = getDOMImplementation() |
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| 122 | doc_type = impl.createDocumentType(CORNODE_NAME, "1.0", "1.0") |
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| 123 | new_doc = impl.createDocument(None, CORNODE_NAME, doc_type) |
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| 124 | top_element = new_doc.documentElement |
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| 125 | else: |
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| 126 | # Create a new element in the document provided |
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| 127 | top_element = doc.createElement(CORNODE_NAME) |
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| 128 | if entry_node is None: |
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| 129 | doc.documentElement.appendChild(top_element) |
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| 130 | else: |
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| 131 | entry_node.appendChild(top_element) |
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| 132 | new_doc = doc |
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| 133 | |
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| 134 | # Version |
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| 135 | attr = new_doc.createAttribute("version") |
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| 136 | attr.nodeValue = '1.0' |
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| 137 | top_element.setAttributeNode(attr) |
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| 138 | |
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| 139 | # Filename |
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| 140 | element = new_doc.createElement("filename") |
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| 141 | if self.file is not None and self.file != '': |
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| 142 | element.appendChild(new_doc.createTextNode(str(self.file))) |
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| 143 | else: |
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| 144 | element.appendChild(new_doc.createTextNode(str(filename))) |
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| 145 | top_element.appendChild(element) |
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| 146 | |
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| 147 | # Timestamp |
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| 148 | element = new_doc.createElement("timestamp") |
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| 149 | # Pretty printed format |
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| 150 | element.appendChild(new_doc.createTextNode(time.ctime(self.timestamp))) |
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| 151 | attr = new_doc.createAttribute("epoch") |
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| 152 | # Epoch value (used in self.fromXML) |
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| 153 | attr.nodeValue = str(self.timestamp) |
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| 154 | element.setAttributeNode(attr) |
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| 155 | top_element.appendChild(element) |
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| 156 | |
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| 157 | # Current state |
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| 158 | state = new_doc.createElement("state") |
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| 159 | top_element.appendChild(state) |
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| 160 | for name, value in self.saved_state.iteritems(): |
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| 161 | element = new_doc.createElement(name) |
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| 162 | element.appendChild(new_doc.createTextNode(str(value))) |
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| 163 | state.appendChild(element) |
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| 164 | |
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| 165 | # Whether or not the extrapolate & transform buttons have been clicked |
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| 166 | element = new_doc.createElement("is_extrapolated") |
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| 167 | top_element.appendChild(element) |
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| 168 | element.appendChild(new_doc.createTextNode(str(int(self.is_extrapolated)))) |
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| 169 | |
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| 170 | element = new_doc.createElement("is_transformed") |
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| 171 | top_element.appendChild(element) |
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| 172 | element.appendChild(new_doc.createTextNode(str(int(self.is_transformed)))) |
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| 173 | |
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| 174 | # Output parameters |
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| 175 | if self.outputs != {} and self.outputs is not None: |
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| 176 | output = new_doc.createElement("output") |
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| 177 | top_element.appendChild(output) |
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| 178 | for item in output_list: |
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| 179 | element = new_doc.createElement(item[0]) |
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| 180 | element.appendChild(new_doc.createTextNode(self.outputs[item[0]])) |
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| 181 | output.appendChild(element) |
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| 182 | |
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| 183 | # Save the file or return the original document with the state |
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| 184 | # data appended |
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| 185 | if doc is None: |
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| 186 | fd = open(filename, 'w') |
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| 187 | fd.write(new_doc.toprettyxml()) |
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| 188 | fd.close() |
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| 189 | return None |
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| 190 | else: |
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| 191 | return new_doc |
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| 192 | |
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| 193 | |
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| 194 | def fromXML(self, node): |
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| 195 | """ |
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| 196 | Load corfunc states from a file |
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| 197 | |
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| 198 | :param node: node of an XML document to read from (optional) |
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| 199 | """ |
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| 200 | if node.get('version') and node.get('version') == '1.0': |
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| 201 | # Parse filename |
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| 202 | entry = get_content('ns:filename', node) |
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| 203 | if entry is not None: |
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| 204 | self.file = entry.text.strip() |
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| 205 | |
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| 206 | # Parse timestamp |
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| 207 | entry = get_content('ns:timestamp', node) |
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| 208 | if entry is not None and entry.get('epoch'): |
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| 209 | try: |
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| 210 | self.timestamp = (entry.get('epoch')) |
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| 211 | except: |
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| 212 | msg = ("CorfuncState.fromXML: Could not read timestamp", |
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| 213 | "\n{}").format(sys.exc_value) |
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| 214 | logging.error(msg) |
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| 215 | |
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| 216 | # Parse current state |
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| 217 | entry = get_content('ns:state', node) |
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| 218 | if entry is not None: |
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| 219 | for item in DEFAULT_STATE.iterkeys(): |
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| 220 | input_field = get_content("ns:{}".format(item), entry) |
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| 221 | if input_field is not None: |
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| 222 | try: |
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| 223 | value = float(input_field.text.strip()) |
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| 224 | except: |
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| 225 | value = None |
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| 226 | self.set_saved_state(name=item, value=value) |
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| 227 | |
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| 228 | # Parse is_extrapolated and is_transformed |
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| 229 | entry = get_content('ns:is_extrapolated', node) |
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| 230 | if entry is not None: |
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| 231 | self.is_extrapolated = bool(int(entry.text.strip())) |
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| 232 | entry = get_content('ns:is_transformed', node) |
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| 233 | if entry is not None: |
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| 234 | self.is_transformed = bool(int(entry.text.strip())) |
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| 235 | |
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| 236 | # Parse outputs |
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| 237 | entry = get_content('ns:output', node) |
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| 238 | if entry is not None: |
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| 239 | for item in output_list: |
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| 240 | parameter = get_content("ns:{}".format(item[0]), entry) |
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| 241 | if parameter is not None: |
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| 242 | self.outputs[item[0]] = parameter.text.strip() |
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| 243 | |
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| 244 | |
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| 245 | |
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| 246 | class Reader(CansasReader): |
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| 247 | """ |
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| 248 | Reads a CanSAS file containing the state of a CorfuncPanel |
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| 249 | """ |
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| 250 | |
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| 251 | type_name = "Corfunc" |
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| 252 | |
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| 253 | type = ["Invariant file (*.inv)|*.inv", |
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| 254 | "SASView file (*.svs)|*.svs"] |
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| 255 | |
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| 256 | ext = ['.cor', '.COR', '.svs', '.SVS'] |
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| 257 | |
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| 258 | def __init__(self, callback): |
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| 259 | self.callback = callback |
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| 260 | self.state = None |
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| 261 | |
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| 262 | def read(self, path): |
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| 263 | """ |
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| 264 | Load data and corfunc information frmo a CanSAS file. |
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| 265 | |
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| 266 | :param path: The file path to read from |
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| 267 | :return: Data1D object, a list of Data1D objects, or None |
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| 268 | :raise IOError: When the file can't be found |
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| 269 | :raise IOError: When the file is an invalid file type |
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| 270 | :raise ValueError: When the length of the data vectors are inconsistent |
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| 271 | """ |
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| 272 | output = [] |
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| 273 | if os.path.isfile(path): |
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| 274 | # Load file |
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| 275 | basename = os.path.basename(path) |
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| 276 | root, ext = os.path.splitext(basename) |
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| 277 | if not ext.lower() in self.ext: |
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| 278 | raise IOError, "{} is not a supported file type".format(ext) |
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| 279 | tree = etree.parse(path, parser=etree.ETCompatXMLParser()) |
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| 280 | root = tree.getroot() |
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| 281 | entry_list = root.xpath('/ns:SASroot/ns:SASentry', |
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| 282 | namespaces={'ns': CANSAS_NS}) |
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| 283 | for entry in entry_list: |
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| 284 | sas_entry, _ = self._parse_entry(entry) |
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| 285 | corstate = self._parse_state(entry) |
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| 286 | |
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| 287 | if corstate != None: |
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| 288 | sas_entry.meta_data['corstate'] = corstate |
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| 289 | sas_entry.filename = corstate.file |
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| 290 | output.append(sas_entry) |
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| 291 | else: |
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| 292 | # File not found |
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| 293 | msg = "{} is not a valid file path or doesn't exist".format(path) |
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| 294 | raise IOError, msg |
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| 295 | |
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| 296 | if len(output) == 0: |
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| 297 | return None |
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| 298 | elif len(output) == 1: |
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| 299 | self.callback(output[0].meta_data['corstate'], datainfo=output[0]) |
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| 300 | return output[0] |
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| 301 | else: |
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| 302 | return output |
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| 303 | |
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| 304 | def write(self, filename, datainfo=None, state=None): |
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| 305 | """ |
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| 306 | Write the content of a Data1D as a CanSAS file. |
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| 307 | |
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| 308 | : param filename: Name of the file to write |
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| 309 | : param datainfo: Data1D object |
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| 310 | : param state: CorfuncState object |
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| 311 | """ |
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| 312 | # Prepare datainfo |
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| 313 | if datainfo is None: |
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| 314 | datainfo = Data1D(x=[], y=[]) |
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| 315 | elif not issubclass(datainfo.__class__, Data1D): |
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| 316 | msg = ("The CanSAS writer expects a Data1D instance. {} was ", |
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| 317 | "provided").format(datainfo.__class__.__name__) |
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| 318 | raise RuntimeError, msg |
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| 319 | if datainfo.title is None or datainfo.title == '': |
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| 320 | datainfo.title = datainfo.name |
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| 321 | if datainfo.run_name == None or datainfo.run_name == '': |
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| 322 | datainfo.run = [str(datainfo.name)] |
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| 323 | datainfo.run_name[0] = datainfo.name |
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| 324 | |
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| 325 | # Create the XMl doc |
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| 326 | doc, sasentry = self._to_xml_doc(datainfo) |
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| 327 | if state is not None: |
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| 328 | doc = state.toXML(doc=doc, entry_node=sasentry) |
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| 329 | |
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| 330 | # Write the XML doc to a file |
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| 331 | fd = open(filename, 'w') |
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| 332 | fd.write(doc.toprettyxml()) |
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| 333 | fd.close() |
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| 334 | |
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| 335 | def get_state(self): |
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| 336 | return self.state |
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| 337 | |
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| 338 | |
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| 339 | def _parse_state(self, entry): |
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| 340 | """ |
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| 341 | Read state data from an XML node |
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| 342 | |
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| 343 | :param entry: The XML node to read from |
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| 344 | :return: CorfuncState object |
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| 345 | """ |
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| 346 | state = None |
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| 347 | try: |
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| 348 | nodes = entry.xpath('ns:{}'.format(CORNODE_NAME), |
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| 349 | namespaces={'ns': CANSAS_NS}) |
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| 350 | if nodes != []: |
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| 351 | state = CorfuncState() |
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| 352 | state.fromXML(nodes[0]) |
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| 353 | except: |
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| 354 | msg = "XML document does not contain CorfuncState information\n{}" |
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| 355 | msg.format(sys.exc_value) |
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| 356 | logging.info(msg) |
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| 357 | return state |
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