| 1 | """ |
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| 2 | This software was developed by the University of Tennessee as part of the |
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| 3 | Distributed Data Analysis of Neutron Scattering Experiments (DANSE) |
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| 4 | project funded by the US National Science Foundation. |
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| 5 | |
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| 6 | See the license text in license.txt |
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| 7 | |
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| 8 | copyright 2008, University of Tennessee |
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| 9 | """ |
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| 10 | |
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| 11 | #TODO: Unit conversion |
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| 12 | #TODO: Store error list |
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| 13 | #TODO: convert from pixel to mm for beam center... |
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| 14 | #TODO: Allow for additional meta data for each section |
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| 15 | #TODO: Notes need to be implemented. They can be any XML structure in version 1.0 |
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| 16 | # Process notes have the same problem. |
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| 17 | |
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| 18 | |
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| 19 | import logging |
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| 20 | import numpy |
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| 21 | import os, sys |
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| 22 | from DataLoader.data_info import Data1D, Collimation, Detector, Process, Aperture |
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| 23 | from xml import xpath |
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| 24 | |
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| 25 | has_converter = True |
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| 26 | try: |
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| 27 | from data_util.nxsunit import Converter |
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| 28 | except: |
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| 29 | has_converter = False |
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| 30 | |
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| 31 | def get_node_text(node): |
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| 32 | """ |
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| 33 | Get the text context of a node |
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| 34 | |
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| 35 | @param node: node to read from |
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| 36 | @return: content, attribute list |
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| 37 | """ |
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| 38 | content = None |
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| 39 | attr = {} |
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| 40 | for item in node.childNodes: |
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| 41 | if item.nodeName.find('text')>=0 \ |
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| 42 | and len(item.nodeValue.strip())>0: |
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| 43 | content = item.nodeValue.strip() |
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| 44 | break |
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| 45 | |
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| 46 | if node.hasAttributes(): |
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| 47 | for i in range(node.attributes.length): |
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| 48 | attr[node.attributes.item(i).nodeName] \ |
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| 49 | = node.attributes.item(i).nodeValue |
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| 50 | |
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| 51 | return content, attr |
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| 52 | |
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| 53 | def get_content(location, node): |
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| 54 | """ |
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| 55 | Get the first instance of the content of a xpath location |
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| 56 | |
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| 57 | @param location: xpath location |
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| 58 | @param node: node to start at |
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| 59 | """ |
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| 60 | value = None |
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| 61 | attr = {} |
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| 62 | nodes = xpath.Evaluate(location, node) |
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| 63 | if len(nodes)>0: |
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| 64 | try: |
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| 65 | # Skip comments and empty lines |
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| 66 | for item in nodes[0].childNodes: |
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| 67 | if item.nodeName.find('text')>=0 \ |
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| 68 | and len(item.nodeValue.strip())>0: |
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| 69 | value = item.nodeValue.strip() |
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| 70 | break |
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| 71 | |
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| 72 | if nodes[0].hasAttributes(): |
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| 73 | for i in range(nodes[0].attributes.length): |
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| 74 | attr[nodes[0].attributes.item(i).nodeName] \ |
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| 75 | = nodes[0].attributes.item(i).nodeValue |
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| 76 | except: |
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| 77 | # problem reading the node. Skip it and return that |
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| 78 | # nothing was found |
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| 79 | logging.error("cansas_reader.get_content: %s\n %s" % (location, sys.exc_value)) |
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| 80 | |
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| 81 | return value, attr |
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| 82 | |
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| 83 | def get_float(location, node): |
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| 84 | """ |
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| 85 | Get the content of a node as a float |
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| 86 | |
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| 87 | @param location: xpath location |
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| 88 | @param node: node to start at |
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| 89 | """ |
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| 90 | value = None |
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| 91 | attr = {} |
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| 92 | content, attr = get_content(location, node) |
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| 93 | if content is not None: |
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| 94 | try: |
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| 95 | value = float(content) |
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| 96 | except: |
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| 97 | # Could not pass, skip and return None |
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| 98 | logging.error("cansas_reader.get_float: could not convert '%s' to float" % content) |
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| 99 | |
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| 100 | return value, attr |
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| 101 | |
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| 102 | def _store_float(location, node, variable, storage): |
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| 103 | """ |
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| 104 | Get the content of a xpath location and store |
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| 105 | the result. Check that the units are compatible |
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| 106 | with the destination. The value is expected to |
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| 107 | be a float. |
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| 108 | |
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| 109 | The xpath location might or might not exist. |
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| 110 | If it does not exist, nothing is done |
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| 111 | |
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| 112 | @param location: xpath location to fetch |
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| 113 | @param node: node to read the data from |
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| 114 | @param variable: name of the data member to store it in [string] |
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| 115 | @param storage: data object that has the 'variable' data member |
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| 116 | |
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| 117 | @raise ValueError: raised when the units are not recognized |
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| 118 | """ |
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| 119 | value, attr = get_float(location, node) |
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| 120 | if value is not None: |
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| 121 | # If the entry has units, check to see that they are |
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| 122 | # compatible with what we currently have in the data object |
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| 123 | if attr.has_key('unit'): |
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| 124 | toks = variable.split('.') |
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| 125 | exec "local_unit = storage.%s_unit.lower()" % toks[0] |
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| 126 | if attr['unit'].lower()!=local_unit: |
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| 127 | if has_converter==True: |
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| 128 | try: |
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| 129 | conv = Converter(attr['unit']) |
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| 130 | exec "storage.%s = %g" % (variable, conv(value, units=local_unit)) |
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| 131 | except: |
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| 132 | raise ValueError, "CanSAS reader: could not convert %s unit [%s]; expecting [%s]\n %s" \ |
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| 133 | % (variable, attr['unit'], local_unit, sys.exc_value) |
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| 134 | else: |
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| 135 | raise ValueError, "CanSAS reader: unrecognized %s unit [%s]; expecting [%s]" \ |
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| 136 | % (variable, attr['unit'], local_unit) |
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| 137 | else: |
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| 138 | exec "storage.%s = value" % variable |
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| 139 | else: |
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| 140 | exec "storage.%s = value" % variable |
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| 141 | |
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| 142 | |
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| 143 | def _store_content(location, node, variable, storage): |
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| 144 | """ |
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| 145 | Get the content of a xpath location and store |
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| 146 | the result. The value is treated as a string. |
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| 147 | |
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| 148 | The xpath location might or might not exist. |
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| 149 | If it does not exist, nothing is done |
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| 150 | |
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| 151 | @param location: xpath location to fetch |
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| 152 | @param node: node to read the data from |
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| 153 | @param variable: name of the data member to store it in [string] |
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| 154 | @param storage: data object that has the 'variable' data member |
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| 155 | """ |
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| 156 | value, attr = get_content(location, node) |
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| 157 | if value is not None: |
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| 158 | exec "storage.%s = value" % variable |
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| 159 | |
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| 160 | |
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| 161 | class Reader: |
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| 162 | """ |
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| 163 | Class to load cansas 1D XML files |
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| 164 | |
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| 165 | Dependencies: |
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| 166 | The CanSas reader requires PyXML 0.8.4 or later. |
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| 167 | """ |
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| 168 | ## CanSAS version |
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| 169 | version = '1.0' |
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| 170 | ## File type |
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| 171 | type = ["CanSAS 1D files (*.xml)|*.xml"] |
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| 172 | ## List of allowed extensions |
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| 173 | ext=['.xml', '.XML'] |
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| 174 | |
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| 175 | def read(self, path): |
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| 176 | """ |
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| 177 | Load data file |
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| 178 | |
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| 179 | @param path: file path |
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| 180 | @return: Data1D object if a single SASentry was found, |
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| 181 | or a list of Data1D objects if multiple entries were found, |
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| 182 | or None of nothing was found |
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| 183 | @raise RuntimeError: when the file can't be opened |
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| 184 | @raise ValueError: when the length of the data vectors are inconsistent |
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| 185 | """ |
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| 186 | from xml.dom.minidom import parse |
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| 187 | |
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| 188 | output = [] |
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| 189 | |
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| 190 | if os.path.isfile(path): |
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| 191 | basename = os.path.basename(path) |
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| 192 | root, extension = os.path.splitext(basename) |
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| 193 | if extension.lower() in self.ext: |
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| 194 | |
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| 195 | dom = parse(path) |
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| 196 | |
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| 197 | # Check the format version number |
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| 198 | nodes = xpath.Evaluate('SASroot', dom) |
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| 199 | if nodes[0].hasAttributes(): |
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| 200 | for i in range(nodes[0].attributes.length): |
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| 201 | if nodes[0].attributes.item(i).nodeName=='version': |
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| 202 | if nodes[0].attributes.item(i).nodeValue != self.version: |
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| 203 | raise ValueError, "cansas_reader: unrecognized version number %s" % \ |
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| 204 | nodes[0].attributes.item(i).nodeValue |
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| 205 | |
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| 206 | entry_list = xpath.Evaluate('SASroot/SASentry', dom) |
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| 207 | for entry in entry_list: |
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| 208 | sas_entry = self._parse_entry(entry) |
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| 209 | sas_entry.filename = basename |
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| 210 | output.append(sas_entry) |
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| 211 | |
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| 212 | else: |
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| 213 | raise RuntimeError, "%s is not a file" % path |
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| 214 | |
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| 215 | # Return output consistent with the loader's api |
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| 216 | if len(output)==0: |
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| 217 | return None |
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| 218 | elif len(output)==1: |
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| 219 | return output[0] |
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| 220 | else: |
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| 221 | return output |
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| 222 | |
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| 223 | def _parse_entry(self, dom): |
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| 224 | """ |
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| 225 | Parse a SASentry |
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| 226 | |
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| 227 | @param node: SASentry node |
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| 228 | @return: Data1D object |
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| 229 | """ |
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| 230 | x = numpy.zeros(0) |
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| 231 | y = numpy.zeros(0) |
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| 232 | |
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| 233 | data_info = Data1D(x, y) |
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| 234 | |
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| 235 | # Look up title |
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| 236 | _store_content('Title', dom, 'title', data_info) |
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| 237 | # Look up run number |
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| 238 | _store_content('Run', dom, 'run', data_info) |
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| 239 | # Look up instrument name |
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| 240 | value, attr = get_content('SASinstrument', dom) |
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| 241 | if attr.has_key('name'): |
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| 242 | data_info.instrument = attr['name'] |
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| 243 | |
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| 244 | note_list = xpath.Evaluate('SASnote', dom) |
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| 245 | for note in note_list: |
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| 246 | try: |
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| 247 | note_value, note_attr = get_node_text(note) |
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| 248 | if note_value is not None: |
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| 249 | data_info.notes.append(note_value) |
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| 250 | except: |
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| 251 | logging.error("cansas_reader.read: error processing entry notes\n %s" % sys.exc_value) |
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| 252 | |
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| 253 | |
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| 254 | # Sample info ################### |
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| 255 | _store_content('SASsample/ID', |
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| 256 | dom, 'ID', data_info.sample) |
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| 257 | _store_float('SASsample/thickness', |
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| 258 | dom, 'thickness', data_info.sample) |
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| 259 | _store_float('SASsample/transmission', |
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| 260 | dom, 'transmission', data_info.sample) |
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| 261 | _store_float('SASsample/temperature', |
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| 262 | dom, 'temperature', data_info.sample) |
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| 263 | nodes = xpath.Evaluate('SASsample/details', dom) |
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| 264 | for item in nodes: |
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| 265 | try: |
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| 266 | detail_value, detail_attr = get_node_text(item) |
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| 267 | if detail_value is not None: |
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| 268 | data_info.sample.details.append(detail_value) |
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| 269 | except: |
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| 270 | logging.error("cansas_reader.read: error processing sample details\n %s" % sys.exc_value) |
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| 271 | |
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| 272 | # Position (as a vector) |
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| 273 | _store_float('SASsample/position/x', |
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| 274 | dom, 'position.x', data_info.sample) |
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| 275 | _store_float('SASsample/position/y', |
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| 276 | dom, 'position.y', data_info.sample) |
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| 277 | _store_float('SASsample/position/z', |
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| 278 | dom, 'position.z', data_info.sample) |
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| 279 | |
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| 280 | # Orientation (as a vector) |
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| 281 | _store_float('SASsample/orientation/roll', |
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| 282 | dom, 'orientation.x', data_info.sample) |
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| 283 | _store_float('SASsample/orientation/pitch', |
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| 284 | dom, 'orientation.y', data_info.sample) |
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| 285 | _store_float('SASsample/orientation/yaw', |
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| 286 | dom, 'orientation.z', data_info.sample) |
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| 287 | |
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| 288 | # Source info ################### |
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| 289 | _store_content('SASinstrument/SASsource/radiation', |
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| 290 | dom, 'radiation', data_info.source) |
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| 291 | _store_content('SASinstrument/SASsource/beam_shape', |
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| 292 | dom, 'beam_shape', data_info.source) |
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| 293 | _store_float('SASinstrument/SASsource/wavelength', |
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| 294 | dom, 'wavelength', data_info.source) |
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| 295 | _store_float('SASinstrument/SASsource/wavelength_min', |
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| 296 | dom, 'wavelength_min', data_info.source) |
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| 297 | _store_float('SASinstrument/SASsource/wavelength_max', |
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| 298 | dom, 'wavelength_max', data_info.source) |
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| 299 | _store_float('SASinstrument/SASsource/wavelength_spread', |
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| 300 | dom, 'wavelength_spread', data_info.source) |
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| 301 | |
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| 302 | # Beam size (as a vector) |
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| 303 | _store_float('SASinstrument/SASsource/beam_size/x', |
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| 304 | dom, 'beam_size.x', data_info.source) |
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| 305 | _store_float('SASinstrument/SASsource/beam_size/y', |
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| 306 | dom, 'beam_size.y', data_info.source) |
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| 307 | _store_float('SASinstrument/SASsource/beam_size/z', |
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| 308 | dom, 'beam_size.z', data_info.source) |
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| 309 | |
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| 310 | # Collimation info ################### |
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| 311 | nodes = xpath.Evaluate('SASinstrument/SAScollimation', dom) |
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| 312 | for item in nodes: |
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| 313 | collim = Collimation() |
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| 314 | _store_float('length', item, 'length', collim) |
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| 315 | |
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| 316 | # Look for apertures |
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| 317 | apert_list = xpath.Evaluate('aperture', item) |
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| 318 | for apert in apert_list: |
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| 319 | aperture = Aperture() |
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| 320 | _store_float('distance', apert, 'distance', aperture) |
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| 321 | _store_float('size/x', apert, 'size.x', aperture) |
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| 322 | _store_float('size/y', apert, 'size.y', aperture) |
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| 323 | _store_float('size/z', apert, 'size.z', aperture) |
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| 324 | |
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| 325 | collim.aperture.append(aperture) |
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| 326 | |
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| 327 | data_info.collimation.append(collim) |
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| 328 | |
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| 329 | # Detector info ###################### |
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| 330 | nodes = xpath.Evaluate('SASinstrument/SASdetector', dom) |
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| 331 | for item in nodes: |
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| 332 | |
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| 333 | detector = Detector() |
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| 334 | |
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| 335 | _store_content('name', item, 'name', detector) |
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| 336 | _store_float('SDD', item, 'distance', detector) |
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| 337 | |
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| 338 | # Detector offset (as a vector) |
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| 339 | _store_float('offset/x', item, 'offset.x', detector) |
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| 340 | _store_float('offset/y', item, 'offset.y', detector) |
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| 341 | _store_float('offset/z', item, 'offset.z', detector) |
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| 342 | |
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| 343 | # Detector orientation (as a vector) |
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| 344 | _store_float('orientation/pitch', item, 'orientation.x', detector) |
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| 345 | _store_float('orientation/yaw', item, 'orientation.y', detector) |
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| 346 | _store_float('orientation/roll', item, 'orientation.z', detector) |
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| 347 | |
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| 348 | # Beam center (as a vector) |
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| 349 | _store_float('beam_center/x', item, 'beam_center.x', detector) |
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| 350 | _store_float('beam_center/y', item, 'beam_center.y', detector) |
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| 351 | _store_float('beam_center/z', item, 'beam_center.z', detector) |
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| 352 | |
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| 353 | # Pixel size (as a vector) |
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| 354 | _store_float('pixel_size/x', item, 'pixel_size.x', detector) |
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| 355 | _store_float('pixel_size/y', item, 'pixel_size.y', detector) |
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| 356 | _store_float('pixel_size/z', item, 'pixel_size.z', detector) |
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| 357 | |
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| 358 | _store_float('slit_length', item, 'slit_length', detector) |
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| 359 | |
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| 360 | data_info.detector.append(detector) |
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| 361 | |
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| 362 | # Processes info ###################### |
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| 363 | nodes = xpath.Evaluate('SASprocess', dom) |
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| 364 | for item in nodes: |
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| 365 | process = Process() |
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| 366 | _store_content('name', item, 'name', process) |
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| 367 | _store_content('date', item, 'date', process) |
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| 368 | _store_content('description', item, 'description', process) |
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| 369 | |
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| 370 | term_list = xpath.Evaluate('term', item) |
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| 371 | for term in term_list: |
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| 372 | try: |
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| 373 | term_value, term_attr = get_node_text(term) |
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| 374 | term_attr['value'] = term_value |
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| 375 | if term_value is not None: |
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| 376 | process.term.append(term_attr) |
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| 377 | except: |
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| 378 | logging.error("cansas_reader.read: error processing process term\n %s" % sys.exc_value) |
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| 379 | |
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| 380 | note_list = xpath.Evaluate('SASprocessnote', item) |
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| 381 | for note in note_list: |
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| 382 | try: |
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| 383 | note_value, note_attr = get_node_text(note) |
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| 384 | if note_value is not None: |
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| 385 | process.notes.append(note_value) |
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| 386 | except: |
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| 387 | logging.error("cansas_reader.read: error processing process notes\n %s" % sys.exc_value) |
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| 388 | |
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| 389 | |
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| 390 | data_info.process.append(process) |
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| 391 | |
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| 392 | |
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| 393 | # Data info ###################### |
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| 394 | nodes = xpath.Evaluate('SASdata/Idata', dom) |
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| 395 | x = numpy.zeros(0) |
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| 396 | y = numpy.zeros(0) |
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| 397 | dx = numpy.zeros(0) |
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| 398 | dy = numpy.zeros(0) |
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| 399 | |
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| 400 | for item in nodes: |
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| 401 | _x, attr = get_float('Q', item) |
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| 402 | _dx, attr = get_float('Qdev', item) |
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| 403 | if _dx == None: |
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| 404 | _dx = 0.0 |
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| 405 | if attr.has_key('unit') and attr['unit'].lower() != data_info.x_unit.lower(): |
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| 406 | raise ValueError, "CanSAS reader: unrecognized %s unit [%s]; expecting [%s]" \ |
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| 407 | % (variable, attr['unit'], local_unit) |
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| 408 | |
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| 409 | _y, attr = get_float('I', item) |
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| 410 | _dy, attr = get_float('Idev', item) |
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| 411 | if _dy == None: |
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| 412 | _dy = 0.0 |
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| 413 | if attr.has_key('unit') and attr['unit'].lower() != data_info.y_unit.lower(): |
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| 414 | raise ValueError, "CanSAS reader: unrecognized %s unit [%s]; expecting [%s]" \ |
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| 415 | % (variable, attr['unit'], local_unit) |
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| 416 | |
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| 417 | if _x is not None and _y is not None: |
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| 418 | x = numpy.append(x, _x) |
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| 419 | y = numpy.append(x, _y) |
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| 420 | dx = numpy.append(x, _dx) |
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| 421 | dy = numpy.append(x, _dy) |
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| 422 | |
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| 423 | data_info.x = x |
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| 424 | data_info.y = y |
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| 425 | data_info.dx = dx |
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| 426 | data_info.dy = dy |
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| 427 | |
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| 428 | data_conv_q = None |
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| 429 | data_conv_i = None |
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| 430 | |
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| 431 | if has_converter == True and data_info.x_unit != '1/A': |
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| 432 | data_conv_q = Converter('1/A') |
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| 433 | # Test it |
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| 434 | data_conv_q(1.0, output.Q_unit) |
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| 435 | |
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| 436 | if has_converter == True and data_info.y_unit != '1/cm': |
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| 437 | data_conv_i = Converter('1/cm') |
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| 438 | # Test it |
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| 439 | data_conv_i(1.0, output.I_unit) |
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| 440 | |
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| 441 | |
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| 442 | if data_conv_q is not None: |
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| 443 | data_info.xaxis("\\rm{Q}", data_info.x_unit) |
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| 444 | else: |
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| 445 | data_info.xaxis("\\rm{Q}", 'A^{-1}') |
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| 446 | if data_conv_i is not None: |
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| 447 | data_info.yaxis("\\{I(Q)}", data_info.y_unit) |
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| 448 | else: |
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| 449 | data_info.yaxis("\\rm{I(Q)}","cm^{-1}") |
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| 450 | |
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| 451 | return data_info |
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| 452 | |
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| 453 | |
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| 454 | if __name__ == "__main__": |
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| 455 | logging.basicConfig(level=logging.ERROR, |
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| 456 | format='%(asctime)s %(levelname)s %(message)s', |
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| 457 | filename='cansas_reader.log', |
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| 458 | filemode='w') |
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| 459 | reader = Reader() |
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| 460 | print reader.read("../test/cansas1d.xml") |
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| 461 | |
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| 462 | |
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| 463 | |
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