| 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 2009, University of Tennessee |
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| 9 | """ |
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| 10 | import time, os |
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| 11 | import logging |
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| 12 | import DataLoader |
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| 13 | from DataLoader.readers.cansas_reader import Reader as CansasReader |
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| 14 | |
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| 15 | PRNODE_NAME = 'pr_inversion' |
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| 16 | |
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| 17 | ## List of P(r) inversion inputs |
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| 18 | in_list= [["nterms", "self.nfunc"], |
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| 19 | ["d_max", "self.d_max"], |
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| 20 | ["alpha", "self.alpha"], |
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| 21 | ["slit_width", "self.width"], |
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| 22 | ["slit_height", "self.height"], |
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| 23 | ["qmin", "self.qmin"], |
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| 24 | ["qmax", "self.qmax"]] |
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| 25 | |
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| 26 | ## List of P(r) inversion outputs |
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| 27 | out_list= [["elapsed", "self.elapsed"], |
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| 28 | ["rg", "self.rg"], |
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| 29 | ["iq0", "self.iq0"], |
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| 30 | ["bck", "self.bck"], |
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| 31 | ["chi2", "self.chi2"], |
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| 32 | ["osc", "self.osc"], |
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| 33 | ["pos", "self.pos"], |
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| 34 | ["pos_err", "self.pos_err"], |
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| 35 | ["alpha_estimate", "self.alpha_estimate"], |
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| 36 | ["nterms_estimate", "self.nterms_estimate"]] |
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| 37 | |
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| 38 | class InversionState(object): |
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| 39 | """ |
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| 40 | Class to hold the state information of the InversionControl panel. |
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| 41 | """ |
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| 42 | def __init__(self): |
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| 43 | """ |
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| 44 | Default values |
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| 45 | """ |
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| 46 | # Input |
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| 47 | self.file = None |
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| 48 | self.estimate_bck = False |
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| 49 | self.timestamp = time.time() |
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| 50 | |
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| 51 | # Inversion parameters |
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| 52 | self.nfunc = None |
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| 53 | self.d_max = None |
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| 54 | self.alpha = None |
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| 55 | |
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| 56 | # Slit parameters |
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| 57 | self.height = None |
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| 58 | self.width = None |
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| 59 | |
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| 60 | # Q range |
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| 61 | self.qmin = None |
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| 62 | self.qmax = None |
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| 63 | |
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| 64 | # Outputs |
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| 65 | self.elapsed = None |
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| 66 | self.rg = None |
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| 67 | self.iq0 = None |
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| 68 | self.bck = None |
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| 69 | self.chi2 = None |
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| 70 | self.osc = None |
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| 71 | self.pos = None |
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| 72 | self.pos_err = None |
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| 73 | |
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| 74 | # Estimates |
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| 75 | self.alpha_estimate = None |
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| 76 | self.nterms_estimate = None |
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| 77 | |
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| 78 | # Data |
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| 79 | self.q = None |
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| 80 | self.iq_obs = None |
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| 81 | self.iq_calc = None |
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| 82 | |
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| 83 | def __str__(self): |
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| 84 | """ |
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| 85 | Pretty print |
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| 86 | |
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| 87 | @return: string representing the state |
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| 88 | """ |
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| 89 | state = "File: %s\n" % self.file |
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| 90 | state += "Timestamp: %s\n" % self.timestamp |
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| 91 | state += "Estimate bck: %s\n" % str(self.estimate_bck) |
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| 92 | state += "No. terms: %s\n" % str(self.nfunc) |
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| 93 | state += "D_max: %s\n" % str(self.d_max) |
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| 94 | state += "Alpha: %s\n" % str(self.alpha) |
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| 95 | |
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| 96 | state += "Slit height: %s\n" % str(self.height) |
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| 97 | state += "Slit width: %s\n" % str(self.width) |
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| 98 | |
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| 99 | state += "Qmin: %s\n" % str(self.qmin) |
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| 100 | state += "Qmax: %s\n" % str(self.qmax) |
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| 101 | |
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| 102 | state += "\nEstimates:\n" |
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| 103 | state += " Alpha: %s\n" % str(self.alpha_estimate) |
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| 104 | state += " Nterms: %s\n" % str(self.nterms_estimate) |
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| 105 | |
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| 106 | state += "\nOutputs:\n" |
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| 107 | state += " Elapsed: %s\n" % str(self.elapsed) |
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| 108 | state += " Rg: %s\n" % str(self.rg) |
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| 109 | state += " I(q=0): %s\n" % str(self.iq0) |
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| 110 | state += " Bck: %s\n" % str(self.bck) |
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| 111 | state += " Chi^2: %s\n" % str(self.chi2) |
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| 112 | state += " Oscillation:%s\n" % str(self.osc) |
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| 113 | state += " Positive: %s\n" % str(self.pos) |
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| 114 | state += " 1-sigma pos:%s\n" % str(self.pos_err) |
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| 115 | |
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| 116 | return state |
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| 117 | |
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| 118 | def toXML(self, file="pr_state.prv", doc=None, entry_node=None): |
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| 119 | """ |
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| 120 | Writes the state of the InversionControl panel to file, as XML. |
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| 121 | |
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| 122 | Compatible with standalone writing, or appending to an |
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| 123 | already existing XML document. In that case, the XML document |
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| 124 | is required. An optional entry node in the XML document may also be given. |
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| 125 | |
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| 126 | @param file: file to write to |
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| 127 | @param doc: XML document object [optional] |
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| 128 | @param entry_node: XML node within the XML document at which we will append the data [optional] |
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| 129 | """ |
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| 130 | from xml.dom.minidom import getDOMImplementation |
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| 131 | |
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| 132 | # Check whether we have to write a standalone XML file |
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| 133 | if doc is None: |
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| 134 | impl = getDOMImplementation() |
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| 135 | |
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| 136 | doc_type = impl.createDocumentType(PRNODE_NAME, "1.0", "1.0") |
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| 137 | |
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| 138 | newdoc = impl.createDocument(None, PRNODE_NAME, doc_type) |
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| 139 | top_element = newdoc.documentElement |
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| 140 | else: |
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| 141 | # We are appending to an existing document |
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| 142 | newdoc = doc |
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| 143 | top_element = newdoc.createElement(PRNODE_NAME) |
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| 144 | if entry_node is None: |
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| 145 | newdoc.documentElement.appendChild(top_element) |
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| 146 | else: |
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| 147 | entry_node.appendChild(top_element) |
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| 148 | |
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| 149 | attr = newdoc.createAttribute("version") |
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| 150 | attr.nodeValue = '1.0' |
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| 151 | top_element.setAttributeNode(attr) |
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| 152 | |
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| 153 | # File name |
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| 154 | if self.file is not None: |
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| 155 | element = newdoc.createElement("filename") |
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| 156 | element.appendChild(newdoc.createTextNode(str(self.file))) |
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| 157 | top_element.appendChild(element) |
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| 158 | |
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| 159 | element = newdoc.createElement("timestamp") |
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| 160 | element.appendChild(newdoc.createTextNode(time.ctime(self.timestamp))) |
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| 161 | attr = newdoc.createAttribute("epoch") |
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| 162 | attr.nodeValue = str(self.timestamp) |
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| 163 | element.setAttributeNode(attr) |
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| 164 | top_element.appendChild(element) |
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| 165 | |
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| 166 | # Inputs |
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| 167 | inputs = newdoc.createElement("inputs") |
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| 168 | top_element.appendChild(inputs) |
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| 169 | |
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| 170 | for item in in_list: |
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| 171 | element = newdoc.createElement(item[0]) |
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| 172 | exec "element.appendChild(newdoc.createTextNode(str(%s)))" % item[1] |
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| 173 | inputs.appendChild(element) |
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| 174 | |
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| 175 | # Outputs |
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| 176 | outputs = newdoc.createElement("outputs") |
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| 177 | top_element.appendChild(outputs) |
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| 178 | |
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| 179 | for item in out_list: |
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| 180 | element = newdoc.createElement(item[0]) |
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| 181 | exec "element.appendChild(newdoc.createTextNode(str(%s)))" % item[1] |
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| 182 | outputs.appendChild(element) |
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| 183 | |
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| 184 | # Save the file |
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| 185 | if doc is None: |
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| 186 | fd = open(file, 'w') |
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| 187 | fd.write(newdoc.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 newdoc.toprettyxml() |
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| 192 | |
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| 193 | def fromXML(self, file=None, node=None): |
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| 194 | """ |
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| 195 | Load a P(r) inversion state from a file |
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| 196 | |
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| 197 | @param file: .prv file |
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| 198 | @param node: node of a XML document to read from |
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| 199 | """ |
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| 200 | if file is not None: |
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| 201 | # Check whether the file is valid |
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| 202 | if not os.path.isfile(file): |
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| 203 | raise RuntimeError, "P(r) reader: cannot open %s" % file |
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| 204 | |
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| 205 | from xml.dom.minidom import parse |
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| 206 | doc = parse(file) |
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| 207 | node = doc.documentElement |
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| 208 | |
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| 209 | if node.tagName == PRNODE_NAME: |
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| 210 | if node.hasAttribute('version')\ |
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| 211 | and node.getAttribute('version') == '1.0': |
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| 212 | |
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| 213 | if node.hasChildNodes(): |
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| 214 | for node in node.childNodes: |
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| 215 | if node.nodeName == 'filename': |
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| 216 | if node.hasChildNodes(): |
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| 217 | self.file = node.childNodes[0].nodeValue.strip() |
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| 218 | elif node.nodeName == 'timestamp': |
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| 219 | if node.hasAttribute('epoch'): |
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| 220 | try: |
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| 221 | self.timestamp = float(node.getAttribute('epoch')) |
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| 222 | except: |
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| 223 | # Could not read timestamp: pass |
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| 224 | pass |
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| 225 | |
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| 226 | # Parse inversion inputs |
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| 227 | elif node.nodeName == 'inputs': |
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| 228 | if node.hasChildNodes(): |
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| 229 | for item in node.childNodes: |
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| 230 | for out in in_list: |
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| 231 | if item.nodeName == out[0]: |
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| 232 | try: |
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| 233 | exec '%s = float(item.childNodes[0].nodeValue.strip())' % out[1] |
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| 234 | except: |
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| 235 | exec '%s = None' % out[1] |
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| 236 | elif item.nodeName == 'estimate_bck': |
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| 237 | try: |
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| 238 | self.estimate_bck = item.childNodes[0].nodeValue.strip()=='True' |
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| 239 | except: |
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| 240 | self.estimate_bck = False |
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| 241 | |
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| 242 | # Parse inversion outputs |
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| 243 | elif node.nodeName == 'outputs': |
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| 244 | if node.hasChildNodes(): |
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| 245 | for item in node.childNodes: |
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| 246 | for out in out_list: |
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| 247 | if item.nodeName == out[0]: |
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| 248 | try: |
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| 249 | exec '%s = float(item.childNodes[0].nodeValue.strip())' % out[1] |
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| 250 | except: |
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| 251 | exec '%s = None' % out[1] |
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| 252 | else: |
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| 253 | raise RuntimeError, "Unsupported P(r) file version" |
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| 254 | |
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| 255 | |
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| 256 | class Reader(CansasReader): |
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| 257 | """ |
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| 258 | Class to load a .prv P(r) inversion file |
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| 259 | """ |
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| 260 | ## File type |
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| 261 | type_name = "P(r)" |
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| 262 | |
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| 263 | ## Wildcards |
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| 264 | type = ["P(r) files (*.prv)|*.prv"] |
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| 265 | ## List of allowed extensions |
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| 266 | ext=['.prv', '.PRV'] |
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| 267 | |
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| 268 | def __init__(self, call_back, cansas=False): |
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| 269 | """ |
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| 270 | Initialize the call-back method to be called |
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| 271 | after we load a file |
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| 272 | @param call_back: call-back method |
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| 273 | @param cansas: True = files will be written/read in CanSAS format |
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| 274 | False = standalone mode |
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| 275 | |
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| 276 | """ |
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| 277 | ## Call back method to be executed after a file is read |
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| 278 | self.call_back = call_back |
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| 279 | ## CanSAS format flag |
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| 280 | self.cansas = cansas |
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| 281 | |
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| 282 | def read(self, path): |
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| 283 | """ |
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| 284 | Load a new P(r) inversion state from file |
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| 285 | |
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| 286 | @param path: file path |
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| 287 | @return: None |
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| 288 | """ |
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| 289 | if self.cansas==True: |
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| 290 | return self._read_cansas(path) |
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| 291 | else: |
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| 292 | return self._read_standalone(path) |
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| 293 | |
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| 294 | def _read_standalone(self, path): |
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| 295 | """ |
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| 296 | Load a new P(r) inversion state from file. |
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| 297 | The P(r) node is assumed to be the top element. |
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| 298 | |
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| 299 | @param path: file path |
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| 300 | @return: None |
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| 301 | """ |
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| 302 | # Read the new state from file |
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| 303 | state = InversionState() |
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| 304 | state.fromXML(file=path) |
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| 305 | |
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| 306 | # Call back to post the new state |
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| 307 | self.call_back(state) |
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| 308 | return None |
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| 309 | |
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| 310 | def _parse_prstate(self, entry): |
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| 311 | """ |
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| 312 | Read a p(r) inversion result from an XML node |
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| 313 | @param entry: XML node to read from |
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| 314 | @return: InversionState object |
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| 315 | """ |
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| 316 | from xml import xpath |
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| 317 | |
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| 318 | # Create an empty state |
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| 319 | state = InversionState() |
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| 320 | |
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| 321 | # Locate the P(r) node |
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| 322 | try: |
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| 323 | nodes = xpath.Evaluate(PRNODE_NAME, entry) |
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| 324 | state.fromXML(node=nodes[0]) |
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| 325 | except: |
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| 326 | #raise RuntimeError, "%s is not a file with P(r) information." % path |
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| 327 | logging.info("XML document does not contain P(r) information.") |
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| 328 | import sys |
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| 329 | print sys.exc_value |
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| 330 | |
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| 331 | return state |
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| 332 | |
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| 333 | def _read_cansas(self, path): |
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| 334 | """ |
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| 335 | Load data and P(r) information from a CanSAS XML file. |
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| 336 | |
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| 337 | @param path: file path |
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| 338 | @return: Data1D object if a single SASentry was found, |
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| 339 | or a list of Data1D objects if multiple entries were found, |
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| 340 | or None of nothing was found |
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| 341 | @raise RuntimeError: when the file can't be opened |
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| 342 | @raise ValueError: when the length of the data vectors are inconsistent |
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| 343 | """ |
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| 344 | from xml.dom.minidom import parse |
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| 345 | from xml import xpath |
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| 346 | output = [] |
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| 347 | |
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| 348 | if os.path.isfile(path): |
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| 349 | basename = os.path.basename(path) |
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| 350 | root, extension = os.path.splitext(basename) |
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| 351 | if extension.lower() in self.ext or \ |
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| 352 | extension.lower() == '.xml': |
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| 353 | |
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| 354 | dom = parse(path) |
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| 355 | |
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| 356 | # Format 1: check whether we have a CanSAS file |
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| 357 | nodes = xpath.Evaluate('SASroot', dom) |
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| 358 | # Check the format version number |
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| 359 | if nodes[0].hasAttributes(): |
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| 360 | for i in range(nodes[0].attributes.length): |
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| 361 | if nodes[0].attributes.item(i).nodeName=='version': |
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| 362 | if nodes[0].attributes.item(i).nodeValue != self.version: |
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| 363 | raise ValueError, "cansas_reader: unrecognized version number %s" % \ |
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| 364 | nodes[0].attributes.item(i).nodeValue |
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| 365 | |
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| 366 | entry_list = xpath.Evaluate('SASroot/SASentry', dom) |
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| 367 | for entry in entry_list: |
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| 368 | sas_entry = self._parse_entry(entry) |
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| 369 | prstate = self._parse_prstate(entry) |
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| 370 | sas_entry.meta_data['prstate'] = prstate |
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| 371 | sas_entry.filename = basename |
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| 372 | output.append(sas_entry) |
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| 373 | else: |
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| 374 | raise RuntimeError, "%s is not a file" % path |
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| 375 | |
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| 376 | # Return output consistent with the loader's api |
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| 377 | if len(output)==0: |
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| 378 | return None |
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| 379 | elif len(output)==1: |
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| 380 | return output[0] |
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| 381 | else: |
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| 382 | return output |
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| 383 | |
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| 384 | |
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| 385 | def write(self, filename, datainfo=None, prstate=None): |
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| 386 | """ |
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| 387 | Write the content of a Data1D as a CanSAS XML file |
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| 388 | |
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| 389 | @param filename: name of the file to write |
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| 390 | @param datainfo: Data1D object |
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| 391 | @param prstate: InversionState object |
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| 392 | """ |
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| 393 | |
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| 394 | # Sanity check |
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| 395 | if self.cansas == True: |
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| 396 | if datainfo is None: |
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| 397 | datainfo = DataLoader.data_info.Data1D(x=[], y=[]) |
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| 398 | elif not datainfo.__class__ == DataLoader.data_info.Data1D: |
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| 399 | raise RuntimeError, "The cansas writer expects a Data1D instance" |
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| 400 | |
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| 401 | # Create basic XML document |
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| 402 | doc, sasentry = self._to_xml_doc(datainfo) |
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| 403 | |
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| 404 | # Add the P(r) information to the XML document |
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| 405 | if prstate is not None: |
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| 406 | prstate.toXML(doc=doc, entry_node=sasentry) |
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| 407 | |
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| 408 | # Write the XML document |
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| 409 | fd = open(filename, 'w') |
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| 410 | fd.write(doc.toprettyxml()) |
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| 411 | fd.close() |
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| 412 | else: |
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| 413 | prstate.toXML(file=filename) |
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| 414 | |
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| 415 | |
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| 416 | if __name__ == "__main__": |
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| 417 | #TODO: turn all this into unit tests |
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| 418 | |
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| 419 | state = InversionState() |
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| 420 | #print state.fromXML('../../test/pr_state.prv') |
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| 421 | print state.fromXML('../../test/test.prv') |
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| 422 | print state |
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| 423 | state.toXML('test_copy.prv') |
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| 424 | |
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| 425 | from DataLoader.loader import Loader |
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| 426 | l = Loader() |
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| 427 | datainfo = l.load("../../test/cansas1d.xml") |
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| 428 | |
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| 429 | def call_back(state): |
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| 430 | print state |
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| 431 | |
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| 432 | reader = Reader(call_back) |
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| 433 | reader.cansas = False |
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| 434 | reader.write("test_copy_from_reader.prv", prstate=state) |
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| 435 | reader.cansas = True |
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| 436 | reader.write("testout.prv", datainfo, state) |
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| 437 | reader.write("testout_wo_datainfo.prv", prstate=state) |
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| 438 | |
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| 439 | # Now try to load things back |
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| 440 | reader.cansas = False |
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| 441 | #print reader.read("test_copy_from_reader.prv") |
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| 442 | reader.cansas = True |
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| 443 | #data = reader.read("testout.prv") |
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| 444 | data = reader.read("testout_wo_datainfo.prv") |
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| 445 | print data |
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| 446 | print data.meta_data['prstate'] |
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| 447 | |
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| 448 | |
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