[a3084ada] | 1 | """ |
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[f60a8c2] | 2 | Module that contains classes to hold information read from |
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[a3084ada] | 3 | reduced data files. |
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[e4f421c] | 4 | |
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[f60a8c2] | 5 | A good description of the data members can be found in |
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[a3084ada] | 6 | the CanSAS 1D XML data format: |
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[e4f421c] | 7 | |
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[a3084ada] | 8 | http://www.smallangles.net/wgwiki/index.php/cansas1d_documentation |
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| 9 | """ |
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[f60a8c2] | 10 | ##################################################################### |
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[0997158f] | 11 | #This software was developed by the University of Tennessee as part of the |
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| 12 | #Distributed Data Analysis of Neutron Scattering Experiments (DANSE) |
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[f60a8c2] | 13 | #project funded by the US National Science Foundation. |
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| 14 | #See the license text in license.txt |
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[0997158f] | 15 | #copyright 2008, University of Tennessee |
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[f60a8c2] | 16 | ###################################################################### |
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[a3084ada] | 17 | |
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| 18 | |
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[b39c817] | 19 | #TODO: Keep track of data manipulation in the 'process' data structure. |
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[579ba85] | 20 | #TODO: This module should be independent of plottables. We should write |
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| 21 | # an adapter class for plottables when needed. |
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[b39c817] | 22 | |
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[79492222] | 23 | #from sas.guitools.plottables import Data1D as plottable_1D |
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[b699768] | 24 | from sas.sascalc.data_util.uncertainty import Uncertainty |
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[9198b83] | 25 | import numpy |
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| 26 | import math |
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[345e7e4] | 27 | |
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| 28 | class plottable_1D(object): |
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| 29 | """ |
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| 30 | Data1D is a place holder for 1D plottables. |
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| 31 | """ |
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| 32 | # The presence of these should be mutually |
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| 33 | # exclusive with the presence of Qdev (dx) |
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| 34 | x = None |
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| 35 | y = None |
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| 36 | dx = None |
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| 37 | dy = None |
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| 38 | ## Slit smearing length |
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| 39 | dxl = None |
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| 40 | ## Slit smearing width |
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| 41 | dxw = None |
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[a9f579c] | 42 | ## SESANS specific params (wavelengths for spin echo length calculation) |
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| 43 | lam = None |
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| 44 | dlam = None |
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[1b82623] | 45 | |
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[579ba85] | 46 | # Units |
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| 47 | _xaxis = '' |
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| 48 | _xunit = '' |
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| 49 | _yaxis = '' |
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| 50 | _yunit = '' |
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[e4f421c] | 51 | |
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[a9f579c] | 52 | def __init__(self, x, y, dx=None, dy=None, dxl=None, dxw=None, lam=None, dlam=None): |
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[2733188] | 53 | self.x = numpy.asarray(x) |
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| 54 | self.y = numpy.asarray(y) |
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[a7a5886] | 55 | if dx is not None: |
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[f60a8c2] | 56 | self.dx = numpy.asarray(dx) |
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| 57 | if dy is not None: |
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[a7a5886] | 58 | self.dy = numpy.asarray(dy) |
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[f60a8c2] | 59 | if dxl is not None: |
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[a7a5886] | 60 | self.dxl = numpy.asarray(dxl) |
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[e4f421c] | 61 | if dxw is not None: |
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[a7a5886] | 62 | self.dxw = numpy.asarray(dxw) |
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[a9f579c] | 63 | if lam is not None: |
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| 64 | self.lam = numpy.asarray(lam) |
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| 65 | if dlam is not None: |
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| 66 | self.dlam = numpy.asarray(dlam) |
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[579ba85] | 67 | |
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| 68 | def xaxis(self, label, unit): |
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[a7a5886] | 69 | """ |
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| 70 | set the x axis label and unit |
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| 71 | """ |
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[579ba85] | 72 | self._xaxis = label |
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| 73 | self._xunit = unit |
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[e4f421c] | 74 | |
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[579ba85] | 75 | def yaxis(self, label, unit): |
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[a7a5886] | 76 | """ |
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| 77 | set the y axis label and unit |
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| 78 | """ |
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[579ba85] | 79 | self._yaxis = label |
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| 80 | self._yunit = unit |
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| 81 | |
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[f60a8c2] | 82 | |
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[e4f421c] | 83 | class plottable_2D(object): |
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[8780e9a] | 84 | """ |
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[0997158f] | 85 | Data2D is a place holder for 2D plottables. |
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[8780e9a] | 86 | """ |
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| 87 | xmin = None |
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| 88 | xmax = None |
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| 89 | ymin = None |
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| 90 | ymax = None |
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[99d1af6] | 91 | data = None |
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[f60a8c2] | 92 | qx_data = None |
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| 93 | qy_data = None |
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| 94 | q_data = None |
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| 95 | err_data = None |
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| 96 | dqx_data = None |
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| 97 | dqy_data = None |
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| 98 | mask = None |
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[e4f421c] | 99 | |
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[99d1af6] | 100 | # Units |
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| 101 | _xaxis = '' |
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| 102 | _xunit = '' |
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| 103 | _yaxis = '' |
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| 104 | _yunit = '' |
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| 105 | _zaxis = '' |
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| 106 | _zunit = '' |
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[e4f421c] | 107 | |
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[a7a5886] | 108 | def __init__(self, data=None, err_data=None, qx_data=None, |
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[f60a8c2] | 109 | qy_data=None, q_data=None, mask=None, |
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| 110 | dqx_data=None, dqy_data=None): |
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[442f42f] | 111 | self.data = numpy.asarray(data) |
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[3cd95c8] | 112 | self.qx_data = numpy.asarray(qx_data) |
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| 113 | self.qy_data = numpy.asarray(qy_data) |
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| 114 | self.q_data = numpy.asarray(q_data) |
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| 115 | self.mask = numpy.asarray(mask) |
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[442f42f] | 116 | self.err_data = numpy.asarray(err_data) |
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[f60a8c2] | 117 | if dqx_data is not None: |
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[e4f421c] | 118 | self.dqx_data = numpy.asarray(dqx_data) |
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[f60a8c2] | 119 | if dqy_data is not None: |
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[e4f421c] | 120 | self.dqy_data = numpy.asarray(dqy_data) |
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| 121 | |
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[99d1af6] | 122 | def xaxis(self, label, unit): |
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[a7a5886] | 123 | """ |
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| 124 | set the x axis label and unit |
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| 125 | """ |
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[99d1af6] | 126 | self._xaxis = label |
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| 127 | self._xunit = unit |
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[e4f421c] | 128 | |
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[99d1af6] | 129 | def yaxis(self, label, unit): |
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[a7a5886] | 130 | """ |
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| 131 | set the y axis label and unit |
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| 132 | """ |
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[99d1af6] | 133 | self._yaxis = label |
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| 134 | self._yunit = unit |
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[e4f421c] | 135 | |
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[99d1af6] | 136 | def zaxis(self, label, unit): |
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[a7a5886] | 137 | """ |
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| 138 | set the z axis label and unit |
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| 139 | """ |
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[99d1af6] | 140 | self._zaxis = label |
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| 141 | self._zunit = unit |
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[de5c813] | 142 | |
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[e4f421c] | 143 | |
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| 144 | class Vector(object): |
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[a3084ada] | 145 | """ |
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[0997158f] | 146 | Vector class to hold multi-dimensional objects |
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[a3084ada] | 147 | """ |
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| 148 | ## x component |
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| 149 | x = None |
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| 150 | ## y component |
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| 151 | y = None |
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| 152 | ## z component |
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| 153 | z = None |
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[e4f421c] | 154 | |
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[a3084ada] | 155 | def __init__(self, x=None, y=None, z=None): |
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| 156 | """ |
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[0997158f] | 157 | Initialization. Components that are not |
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| 158 | set a set to None by default. |
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[e4f421c] | 159 | |
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[0997158f] | 160 | :param x: x component |
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| 161 | :param y: y component |
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| 162 | :param z: z component |
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[a3084ada] | 163 | """ |
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| 164 | self.x = x |
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| 165 | self.y = y |
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| 166 | self.z = z |
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[e4f421c] | 167 | |
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[a3084ada] | 168 | def __str__(self): |
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[a7a5886] | 169 | msg = "x = %s\ty = %s\tz = %s" % (str(self.x), str(self.y), str(self.z)) |
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| 170 | return msg |
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[a3084ada] | 171 | |
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[e4f421c] | 172 | |
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| 173 | class Detector(object): |
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[a3084ada] | 174 | """ |
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[0997158f] | 175 | Class to hold detector information |
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[a3084ada] | 176 | """ |
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| 177 | ## Name of the instrument [string] |
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[fe78c7b] | 178 | name = None |
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[a3084ada] | 179 | ## Sample to detector distance [float] [mm] |
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| 180 | distance = None |
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[b39c817] | 181 | distance_unit = 'mm' |
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[f60a8c2] | 182 | ## Offset of this detector position in X, Y, |
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| 183 | #(and Z if necessary) [Vector] [mm] |
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[d6513cd] | 184 | offset = None |
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[b39c817] | 185 | offset_unit = 'm' |
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[a7a5886] | 186 | ## Orientation (rotation) of this detector in roll, |
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| 187 | # pitch, and yaw [Vector] [degrees] |
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[d6513cd] | 188 | orientation = None |
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[8780e9a] | 189 | orientation_unit = 'degree' |
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[f60a8c2] | 190 | ## Center of the beam on the detector in X and Y |
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[a7a5886] | 191 | #(and Z if necessary) [Vector] [mm] |
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[d6513cd] | 192 | beam_center = None |
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[8780e9a] | 193 | beam_center_unit = 'mm' |
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[a3084ada] | 194 | ## Pixel size in X, Y, (and Z if necessary) [Vector] [mm] |
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[d6513cd] | 195 | pixel_size = None |
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[8780e9a] | 196 | pixel_size_unit = 'mm' |
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[a3084ada] | 197 | ## Slit length of the instrument for this detector.[float] [mm] |
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| 198 | slit_length = None |
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[2e9b98c] | 199 | slit_length_unit = 'mm' |
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[e4f421c] | 200 | |
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[d6513cd] | 201 | def __init__(self): |
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| 202 | """ |
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[0997158f] | 203 | Initialize class attribute that are objects... |
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[d6513cd] | 204 | """ |
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[e4f421c] | 205 | self.offset = Vector() |
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[d6513cd] | 206 | self.orientation = Vector() |
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| 207 | self.beam_center = Vector() |
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[e4f421c] | 208 | self.pixel_size = Vector() |
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| 209 | |
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[8780e9a] | 210 | def __str__(self): |
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[e4f421c] | 211 | _str = "Detector:\n" |
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[8780e9a] | 212 | _str += " Name: %s\n" % self.name |
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| 213 | _str += " Distance: %s [%s]\n" % \ |
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| 214 | (str(self.distance), str(self.distance_unit)) |
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| 215 | _str += " Offset: %s [%s]\n" % \ |
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| 216 | (str(self.offset), str(self.offset_unit)) |
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| 217 | _str += " Orientation: %s [%s]\n" % \ |
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| 218 | (str(self.orientation), str(self.orientation_unit)) |
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| 219 | _str += " Beam center: %s [%s]\n" % \ |
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| 220 | (str(self.beam_center), str(self.beam_center_unit)) |
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| 221 | _str += " Pixel size: %s [%s]\n" % \ |
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| 222 | (str(self.pixel_size), str(self.pixel_size_unit)) |
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| 223 | _str += " Slit length: %s [%s]\n" % \ |
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| 224 | (str(self.slit_length), str(self.slit_length_unit)) |
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| 225 | return _str |
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[a3084ada] | 226 | |
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[f60a8c2] | 227 | |
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[e4f421c] | 228 | class Aperture(object): |
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[4c00964] | 229 | ## Name |
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[579ba85] | 230 | name = None |
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[4c00964] | 231 | ## Type |
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[579ba85] | 232 | type = None |
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| 233 | ## Size name |
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| 234 | size_name = None |
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[4c00964] | 235 | ## Aperture size [Vector] |
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[d6513cd] | 236 | size = None |
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| 237 | size_unit = 'mm' |
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[4c00964] | 238 | ## Aperture distance [float] |
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[d6513cd] | 239 | distance = None |
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| 240 | distance_unit = 'mm' |
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[e4f421c] | 241 | |
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[d6513cd] | 242 | def __init__(self): |
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| 243 | self.size = Vector() |
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[e4f421c] | 244 | |
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| 245 | |
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| 246 | class Collimation(object): |
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[a3084ada] | 247 | """ |
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[0997158f] | 248 | Class to hold collimation information |
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[a3084ada] | 249 | """ |
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[4c00964] | 250 | ## Name |
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[fe78c7b] | 251 | name = None |
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[a3084ada] | 252 | ## Length [float] [mm] |
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| 253 | length = None |
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[8780e9a] | 254 | length_unit = 'mm' |
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| 255 | ## Aperture |
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[d6513cd] | 256 | aperture = None |
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[e4f421c] | 257 | |
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[d6513cd] | 258 | def __init__(self): |
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| 259 | self.aperture = [] |
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[e4f421c] | 260 | |
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[8780e9a] | 261 | def __str__(self): |
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| 262 | _str = "Collimation:\n" |
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| 263 | _str += " Length: %s [%s]\n" % \ |
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| 264 | (str(self.length), str(self.length_unit)) |
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| 265 | for item in self.aperture: |
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| 266 | _str += " Aperture size:%s [%s]\n" % \ |
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| 267 | (str(item.size), str(item.size_unit)) |
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| 268 | _str += " Aperture_dist:%s [%s]\n" % \ |
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| 269 | (str(item.distance), str(item.distance_unit)) |
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| 270 | return _str |
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[a3084ada] | 271 | |
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[f60a8c2] | 272 | |
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[e4f421c] | 273 | class Source(object): |
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[a3084ada] | 274 | """ |
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[0997158f] | 275 | Class to hold source information |
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[f60a8c2] | 276 | """ |
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[4c00964] | 277 | ## Name |
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[579ba85] | 278 | name = None |
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[a3084ada] | 279 | ## Radiation type [string] |
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[579ba85] | 280 | radiation = None |
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| 281 | ## Beam size name |
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| 282 | beam_size_name = None |
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[a3084ada] | 283 | ## Beam size [Vector] [mm] |
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[d6513cd] | 284 | beam_size = None |
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[8780e9a] | 285 | beam_size_unit = 'mm' |
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[a3084ada] | 286 | ## Beam shape [string] |
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[579ba85] | 287 | beam_shape = None |
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[a3084ada] | 288 | ## Wavelength [float] [Angstrom] |
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| 289 | wavelength = None |
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[8780e9a] | 290 | wavelength_unit = 'A' |
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[a3084ada] | 291 | ## Minimum wavelength [float] [Angstrom] |
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| 292 | wavelength_min = None |
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[8780e9a] | 293 | wavelength_min_unit = 'nm' |
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[a3084ada] | 294 | ## Maximum wavelength [float] [Angstrom] |
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| 295 | wavelength_max = None |
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[8780e9a] | 296 | wavelength_max_unit = 'nm' |
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[a3084ada] | 297 | ## Wavelength spread [float] [Angstrom] |
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| 298 | wavelength_spread = None |
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[8780e9a] | 299 | wavelength_spread_unit = 'percent' |
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[e4f421c] | 300 | |
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[d6513cd] | 301 | def __init__(self): |
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| 302 | self.beam_size = Vector() |
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[e4f421c] | 303 | |
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[8780e9a] | 304 | def __str__(self): |
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[e4f421c] | 305 | _str = "Source:\n" |
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[8780e9a] | 306 | _str += " Radiation: %s\n" % str(self.radiation) |
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| 307 | _str += " Shape: %s\n" % str(self.beam_shape) |
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| 308 | _str += " Wavelength: %s [%s]\n" % \ |
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| 309 | (str(self.wavelength), str(self.wavelength_unit)) |
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| 310 | _str += " Waveln_min: %s [%s]\n" % \ |
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| 311 | (str(self.wavelength_min), str(self.wavelength_min_unit)) |
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| 312 | _str += " Waveln_max: %s [%s]\n" % \ |
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| 313 | (str(self.wavelength_max), str(self.wavelength_max_unit)) |
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| 314 | _str += " Waveln_spread:%s [%s]\n" % \ |
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| 315 | (str(self.wavelength_spread), str(self.wavelength_spread_unit)) |
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| 316 | _str += " Beam_size: %s [%s]\n" % \ |
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| 317 | (str(self.beam_size), str(self.beam_size_unit)) |
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| 318 | return _str |
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[e4f421c] | 319 | |
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| 320 | |
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[f60a8c2] | 321 | """ |
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[0997158f] | 322 | Definitions of radiation types |
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[a3084ada] | 323 | """ |
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[e4f421c] | 324 | NEUTRON = 'neutron' |
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| 325 | XRAY = 'x-ray' |
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| 326 | MUON = 'muon' |
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[a3084ada] | 327 | ELECTRON = 'electron' |
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[e4f421c] | 328 | |
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| 329 | |
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| 330 | class Sample(object): |
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[a3084ada] | 331 | """ |
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[0997158f] | 332 | Class to hold the sample description |
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[a3084ada] | 333 | """ |
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[579ba85] | 334 | ## Short name for sample |
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| 335 | name = '' |
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[a3084ada] | 336 | ## ID |
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| 337 | ID = '' |
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| 338 | ## Thickness [float] [mm] |
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| 339 | thickness = None |
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[8780e9a] | 340 | thickness_unit = 'mm' |
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| 341 | ## Transmission [float] [fraction] |
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[a3084ada] | 342 | transmission = None |
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[b3efb7d] | 343 | ## Temperature [float] [No Default] |
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[a3084ada] | 344 | temperature = None |
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[b3efb7d] | 345 | temperature_unit = None |
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[a3084ada] | 346 | ## Position [Vector] [mm] |
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[d6513cd] | 347 | position = None |
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[8780e9a] | 348 | position_unit = 'mm' |
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[a3084ada] | 349 | ## Orientation [Vector] [degrees] |
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[d6513cd] | 350 | orientation = None |
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[8780e9a] | 351 | orientation_unit = 'degree' |
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[a3084ada] | 352 | ## Details |
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[d6513cd] | 353 | details = None |
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[e4f421c] | 354 | |
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[d6513cd] | 355 | def __init__(self): |
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[e4f421c] | 356 | self.position = Vector() |
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[d6513cd] | 357 | self.orientation = Vector() |
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[e4f421c] | 358 | self.details = [] |
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| 359 | |
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[8780e9a] | 360 | def __str__(self): |
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[e4f421c] | 361 | _str = "Sample:\n" |
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[8780e9a] | 362 | _str += " ID: %s\n" % str(self.ID) |
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| 363 | _str += " Transmission: %s\n" % str(self.transmission) |
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| 364 | _str += " Thickness: %s [%s]\n" % \ |
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| 365 | (str(self.thickness), str(self.thickness_unit)) |
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| 366 | _str += " Temperature: %s [%s]\n" % \ |
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| 367 | (str(self.temperature), str(self.temperature_unit)) |
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| 368 | _str += " Position: %s [%s]\n" % \ |
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| 369 | (str(self.position), str(self.position_unit)) |
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| 370 | _str += " Orientation: %s [%s]\n" % \ |
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| 371 | (str(self.orientation), str(self.orientation_unit)) |
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[e4f421c] | 372 | |
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[8780e9a] | 373 | _str += " Details:\n" |
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| 374 | for item in self.details: |
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| 375 | _str += " %s\n" % item |
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[e4f421c] | 376 | |
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[8780e9a] | 377 | return _str |
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[e4f421c] | 378 | |
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| 379 | |
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| 380 | class Process(object): |
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[8780e9a] | 381 | """ |
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[0997158f] | 382 | Class that holds information about the processes |
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| 383 | performed on the data. |
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[8780e9a] | 384 | """ |
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| 385 | name = '' |
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| 386 | date = '' |
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[a7a5886] | 387 | description = '' |
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[d6513cd] | 388 | term = None |
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| 389 | notes = None |
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[e4f421c] | 390 | |
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[d6513cd] | 391 | def __init__(self): |
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| 392 | self.term = [] |
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| 393 | self.notes = [] |
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[e4f421c] | 394 | |
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[3a5f7c8] | 395 | def is_empty(self): |
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| 396 | """ |
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| 397 | Return True if the object is empty |
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| 398 | """ |
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| 399 | return len(self.name) == 0 and len(self.date) == 0 and len(self.description) == 0 \ |
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| 400 | and len(self.term) == 0 and len(self.notes) == 0 |
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[a4deca6] | 401 | |
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[3a5f7c8] | 402 | def single_line_desc(self): |
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| 403 | """ |
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| 404 | Return a single line string representing the process |
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| 405 | """ |
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| 406 | return "%s %s %s" % (self.name, self.date, self.description) |
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[a4deca6] | 407 | |
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[8780e9a] | 408 | def __str__(self): |
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[e4f421c] | 409 | _str = "Process:\n" |
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[8780e9a] | 410 | _str += " Name: %s\n" % self.name |
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| 411 | _str += " Date: %s\n" % self.date |
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| 412 | _str += " Description: %s\n" % self.description |
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| 413 | for item in self.term: |
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| 414 | _str += " Term: %s\n" % item |
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| 415 | for item in self.notes: |
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| 416 | _str += " Note: %s\n" % item |
---|
| 417 | return _str |
---|
[e4f421c] | 418 | |
---|
| 419 | |
---|
| 420 | class TransmissionSpectrum(object): |
---|
[be577e7] | 421 | """ |
---|
| 422 | Class that holds information about transmission spectrum |
---|
| 423 | for white beams and spallation sources. |
---|
| 424 | """ |
---|
| 425 | name = '' |
---|
| 426 | timestamp = '' |
---|
| 427 | ## Wavelength (float) [A] |
---|
| 428 | wavelength = None |
---|
| 429 | wavelength_unit = 'A' |
---|
| 430 | ## Transmission (float) [unit less] |
---|
| 431 | transmission = None |
---|
| 432 | transmission_unit = '' |
---|
| 433 | ## Transmission Deviation (float) [unit less] |
---|
| 434 | transmission_deviation = None |
---|
| 435 | transmission_deviation_unit = '' |
---|
[e4f421c] | 436 | |
---|
[be577e7] | 437 | def __init__(self): |
---|
| 438 | self.wavelength = [] |
---|
| 439 | self.transmission = [] |
---|
| 440 | self.transmission_deviation = [] |
---|
[e4f421c] | 441 | |
---|
[be577e7] | 442 | def __str__(self): |
---|
[e4f421c] | 443 | _str = "Transmission Spectrum:\n" |
---|
[76cd1ae] | 444 | _str += " Name: \t{0}\n".format(self.name) |
---|
| 445 | _str += " Timestamp: \t{0}\n".format(self.timestamp) |
---|
| 446 | _str += " Wavelength unit: \t{0}\n".format(self.wavelength_unit) |
---|
| 447 | _str += " Transmission unit:\t{0}\n".format(self.transmission_unit) |
---|
| 448 | _str += " Trans. Dev. unit: \t{0}\n".format(\ |
---|
| 449 | self.transmission_deviation_unit) |
---|
| 450 | length_list = [len(self.wavelength), len(self.transmission), \ |
---|
| 451 | len(self.transmission_deviation)] |
---|
| 452 | _str += " Number of Pts: \t{0}\n".format(max(length_list)) |
---|
[be577e7] | 453 | return _str |
---|
[e4f421c] | 454 | |
---|
| 455 | |
---|
| 456 | class DataInfo(object): |
---|
[a3084ada] | 457 | """ |
---|
[0997158f] | 458 | Class to hold the data read from a file. |
---|
| 459 | It includes four blocks of data for the |
---|
| 460 | instrument description, the sample description, |
---|
| 461 | the data itself and any other meta data. |
---|
[a3084ada] | 462 | """ |
---|
[f60a8c2] | 463 | ## Title |
---|
[e4f421c] | 464 | title = '' |
---|
[a3084ada] | 465 | ## Run number |
---|
[e4f421c] | 466 | run = None |
---|
[579ba85] | 467 | ## Run name |
---|
[e4f421c] | 468 | run_name = None |
---|
[a3084ada] | 469 | ## File name |
---|
[e4f421c] | 470 | filename = '' |
---|
[a3084ada] | 471 | ## Notes |
---|
[e4f421c] | 472 | notes = None |
---|
[a3084ada] | 473 | ## Processes (Action on the data) |
---|
[e4f421c] | 474 | process = None |
---|
[8780e9a] | 475 | ## Instrument name |
---|
| 476 | instrument = '' |
---|
[a3084ada] | 477 | ## Detector information |
---|
[e4f421c] | 478 | detector = None |
---|
[a3084ada] | 479 | ## Sample information |
---|
[e4f421c] | 480 | sample = None |
---|
[a3084ada] | 481 | ## Source information |
---|
[e4f421c] | 482 | source = None |
---|
[8780e9a] | 483 | ## Collimation information |
---|
[d6513cd] | 484 | collimation = None |
---|
[be577e7] | 485 | ## Transmission Spectrum INfo |
---|
| 486 | trans_spectrum = None |
---|
[a3084ada] | 487 | ## Additional meta-data |
---|
[e4f421c] | 488 | meta_data = None |
---|
[8780e9a] | 489 | ## Loading errors |
---|
[d6513cd] | 490 | errors = None |
---|
[e4f421c] | 491 | |
---|
[b99ac227] | 492 | def __init__(self): |
---|
| 493 | """ |
---|
[0997158f] | 494 | Initialization |
---|
[b99ac227] | 495 | """ |
---|
[e4f421c] | 496 | ## Title |
---|
| 497 | self.title = '' |
---|
[b99ac227] | 498 | ## Run number |
---|
[e4f421c] | 499 | self.run = [] |
---|
| 500 | self.run_name = {} |
---|
[b99ac227] | 501 | ## File name |
---|
[e4f421c] | 502 | self.filename = '' |
---|
[b99ac227] | 503 | ## Notes |
---|
[e4f421c] | 504 | self.notes = [] |
---|
[b99ac227] | 505 | ## Processes (Action on the data) |
---|
[e4f421c] | 506 | self.process = [] |
---|
[b99ac227] | 507 | ## Instrument name |
---|
| 508 | self.instrument = '' |
---|
| 509 | ## Detector information |
---|
[e4f421c] | 510 | self.detector = [] |
---|
[b99ac227] | 511 | ## Sample information |
---|
[e4f421c] | 512 | self.sample = Sample() |
---|
[b99ac227] | 513 | ## Source information |
---|
[e4f421c] | 514 | self.source = Source() |
---|
[b99ac227] | 515 | ## Collimation information |
---|
| 516 | self.collimation = [] |
---|
[be577e7] | 517 | ## Transmission Spectrum |
---|
[76cd1ae] | 518 | self.trans_spectrum = [] |
---|
[b99ac227] | 519 | ## Additional meta-data |
---|
[e4f421c] | 520 | self.meta_data = {} |
---|
[b99ac227] | 521 | ## Loading errors |
---|
[f60a8c2] | 522 | self.errors = [] |
---|
[e4f421c] | 523 | |
---|
[99abf5d] | 524 | def append_empty_process(self): |
---|
[67c7e89] | 525 | """ |
---|
| 526 | """ |
---|
| 527 | self.process.append(Process()) |
---|
[e4f421c] | 528 | |
---|
[67c7e89] | 529 | def add_notes(self, message=""): |
---|
| 530 | """ |
---|
| 531 | Add notes to datainfo |
---|
| 532 | """ |
---|
| 533 | self.notes.append(message) |
---|
[e4f421c] | 534 | |
---|
[99d1af6] | 535 | def __str__(self): |
---|
| 536 | """ |
---|
[0997158f] | 537 | Nice printout |
---|
[99d1af6] | 538 | """ |
---|
[e4f421c] | 539 | _str = "File: %s\n" % self.filename |
---|
[99d1af6] | 540 | _str += "Title: %s\n" % self.title |
---|
| 541 | _str += "Run: %s\n" % str(self.run) |
---|
| 542 | _str += "Instrument: %s\n" % str(self.instrument) |
---|
| 543 | _str += "%s\n" % str(self.sample) |
---|
| 544 | _str += "%s\n" % str(self.source) |
---|
| 545 | for item in self.detector: |
---|
| 546 | _str += "%s\n" % str(item) |
---|
| 547 | for item in self.collimation: |
---|
| 548 | _str += "%s\n" % str(item) |
---|
| 549 | for item in self.process: |
---|
| 550 | _str += "%s\n" % str(item) |
---|
| 551 | for item in self.notes: |
---|
| 552 | _str += "%s\n" % str(item) |
---|
[76cd1ae] | 553 | for item in self.trans_spectrum: |
---|
| 554 | _str += "%s\n" % str(item) |
---|
[99d1af6] | 555 | return _str |
---|
[e4f421c] | 556 | |
---|
[b39c817] | 557 | # Private method to perform operation. Not implemented for DataInfo, |
---|
| 558 | # but should be implemented for each data class inherited from DataInfo |
---|
| 559 | # that holds actual data (ex.: Data1D) |
---|
[f60a8c2] | 560 | def _perform_operation(self, other, operation): |
---|
[a7a5886] | 561 | """ |
---|
| 562 | Private method to perform operation. Not implemented for DataInfo, |
---|
| 563 | but should be implemented for each data class inherited from DataInfo |
---|
| 564 | that holds actual data (ex.: Data1D) |
---|
| 565 | """ |
---|
| 566 | return NotImplemented |
---|
[e4f421c] | 567 | |
---|
[365aa1ed] | 568 | def _perform_union(self, other): |
---|
| 569 | """ |
---|
| 570 | Private method to perform union operation. Not implemented for DataInfo, |
---|
| 571 | but should be implemented for each data class inherited from DataInfo |
---|
| 572 | that holds actual data (ex.: Data1D) |
---|
| 573 | """ |
---|
| 574 | return NotImplemented |
---|
[b39c817] | 575 | |
---|
| 576 | def __add__(self, other): |
---|
| 577 | """ |
---|
[0997158f] | 578 | Add two data sets |
---|
[e4f421c] | 579 | |
---|
[0997158f] | 580 | :param other: data set to add to the current one |
---|
| 581 | :return: new data set |
---|
| 582 | :raise ValueError: raised when two data sets are incompatible |
---|
[b39c817] | 583 | """ |
---|
[a7a5886] | 584 | def operation(a, b): |
---|
| 585 | return a + b |
---|
[b39c817] | 586 | return self._perform_operation(other, operation) |
---|
[e4f421c] | 587 | |
---|
[b39c817] | 588 | def __radd__(self, other): |
---|
| 589 | """ |
---|
[0997158f] | 590 | Add two data sets |
---|
[e4f421c] | 591 | |
---|
[0997158f] | 592 | :param other: data set to add to the current one |
---|
| 593 | :return: new data set |
---|
| 594 | :raise ValueError: raised when two data sets are incompatible |
---|
[b39c817] | 595 | """ |
---|
[a7a5886] | 596 | def operation(a, b): |
---|
| 597 | return b + a |
---|
[b39c817] | 598 | return self._perform_operation(other, operation) |
---|
[e4f421c] | 599 | |
---|
[b39c817] | 600 | def __sub__(self, other): |
---|
| 601 | """ |
---|
[0997158f] | 602 | Subtract two data sets |
---|
[e4f421c] | 603 | |
---|
[0997158f] | 604 | :param other: data set to subtract from the current one |
---|
| 605 | :return: new data set |
---|
| 606 | :raise ValueError: raised when two data sets are incompatible |
---|
[b39c817] | 607 | """ |
---|
[a7a5886] | 608 | def operation(a, b): |
---|
| 609 | return a - b |
---|
[b39c817] | 610 | return self._perform_operation(other, operation) |
---|
[e4f421c] | 611 | |
---|
[b39c817] | 612 | def __rsub__(self, other): |
---|
| 613 | """ |
---|
[0997158f] | 614 | Subtract two data sets |
---|
[e4f421c] | 615 | |
---|
[0997158f] | 616 | :param other: data set to subtract from the current one |
---|
| 617 | :return: new data set |
---|
| 618 | :raise ValueError: raised when two data sets are incompatible |
---|
[b39c817] | 619 | """ |
---|
[a7a5886] | 620 | def operation(a, b): |
---|
| 621 | return b - a |
---|
[b39c817] | 622 | return self._perform_operation(other, operation) |
---|
[e4f421c] | 623 | |
---|
[b39c817] | 624 | def __mul__(self, other): |
---|
| 625 | """ |
---|
[0997158f] | 626 | Multiply two data sets |
---|
[e4f421c] | 627 | |
---|
[0997158f] | 628 | :param other: data set to subtract from the current one |
---|
| 629 | :return: new data set |
---|
| 630 | :raise ValueError: raised when two data sets are incompatible |
---|
[b39c817] | 631 | """ |
---|
[a7a5886] | 632 | def operation(a, b): |
---|
| 633 | return a * b |
---|
[b39c817] | 634 | return self._perform_operation(other, operation) |
---|
[e4f421c] | 635 | |
---|
[b39c817] | 636 | def __rmul__(self, other): |
---|
| 637 | """ |
---|
[0997158f] | 638 | Multiply two data sets |
---|
[e4f421c] | 639 | |
---|
[0997158f] | 640 | :param other: data set to subtract from the current one |
---|
| 641 | :return: new data set |
---|
| 642 | :raise ValueError: raised when two data sets are incompatible |
---|
[b39c817] | 643 | """ |
---|
[a7a5886] | 644 | def operation(a, b): |
---|
| 645 | return b * a |
---|
[b39c817] | 646 | return self._perform_operation(other, operation) |
---|
[e4f421c] | 647 | |
---|
[b39c817] | 648 | def __div__(self, other): |
---|
| 649 | """ |
---|
[0997158f] | 650 | Divided a data set by another |
---|
[e4f421c] | 651 | |
---|
[0997158f] | 652 | :param other: data set that the current one is divided by |
---|
| 653 | :return: new data set |
---|
| 654 | :raise ValueError: raised when two data sets are incompatible |
---|
[b39c817] | 655 | """ |
---|
[a7a5886] | 656 | def operation(a, b): |
---|
| 657 | return a/b |
---|
[b39c817] | 658 | return self._perform_operation(other, operation) |
---|
[e4f421c] | 659 | |
---|
[b39c817] | 660 | def __rdiv__(self, other): |
---|
| 661 | """ |
---|
[0997158f] | 662 | Divided a data set by another |
---|
[e4f421c] | 663 | |
---|
[0997158f] | 664 | :param other: data set that the current one is divided by |
---|
| 665 | :return: new data set |
---|
| 666 | :raise ValueError: raised when two data sets are incompatible |
---|
[b39c817] | 667 | """ |
---|
[a7a5886] | 668 | def operation(a, b): |
---|
| 669 | return b/a |
---|
[f60a8c2] | 670 | return self._perform_operation(other, operation) |
---|
[e4f421c] | 671 | |
---|
[a48842a2] | 672 | def __or__(self, other): |
---|
| 673 | """ |
---|
| 674 | Union a data set with another |
---|
[e4f421c] | 675 | |
---|
[a48842a2] | 676 | :param other: data set to be unified |
---|
| 677 | :return: new data set |
---|
| 678 | :raise ValueError: raised when two data sets are incompatible |
---|
| 679 | """ |
---|
| 680 | return self._perform_union(other) |
---|
[e4f421c] | 681 | |
---|
[a48842a2] | 682 | def __ror__(self, other): |
---|
| 683 | """ |
---|
| 684 | Union a data set with another |
---|
[e4f421c] | 685 | |
---|
[a48842a2] | 686 | :param other: data set to be unified |
---|
| 687 | :return: new data set |
---|
| 688 | :raise ValueError: raised when two data sets are incompatible |
---|
| 689 | """ |
---|
| 690 | return self._perform_union(other) |
---|
[e4f421c] | 691 | |
---|
[a3084ada] | 692 | class Data1D(plottable_1D, DataInfo): |
---|
| 693 | """ |
---|
[0997158f] | 694 | 1D data class |
---|
[a3084ada] | 695 | """ |
---|
[a9f579c] | 696 | def __init__(self, x=None, y=None, dx=None, dy=None, lam=None, dlam=None, isSesans=False): |
---|
| 697 | self.isSesans = isSesans |
---|
[b99ac227] | 698 | DataInfo.__init__(self) |
---|
[a9f579c] | 699 | plottable_1D.__init__(self, x, y, dx, dy,None, None, lam, dlam) |
---|
| 700 | if self.isSesans: |
---|
| 701 | x_unit = 'A' |
---|
| 702 | y_unit = 'pol' |
---|
| 703 | elif not self.isSesans: # it's SANS data! (Could also be simple else statement, but i prefer exhaustive conditionals...-JHB) |
---|
| 704 | x_unit = '1/A' |
---|
| 705 | y_unit = '1/cm' |
---|
| 706 | else: # and if it's neither, you get punished! |
---|
| 707 | raise(TypeError,'This is neither SANS nor SESANS data, what the hell are you doing??') |
---|
[e4f421c] | 708 | |
---|
[a3084ada] | 709 | def __str__(self): |
---|
| 710 | """ |
---|
[0997158f] | 711 | Nice printout |
---|
[a3084ada] | 712 | """ |
---|
[e4f421c] | 713 | _str = "%s\n" % DataInfo.__str__(self) |
---|
[a3084ada] | 714 | _str += "Data:\n" |
---|
| 715 | _str += " Type: %s\n" % self.__class__.__name__ |
---|
| 716 | _str += " X-axis: %s\t[%s]\n" % (self._xaxis, self._xunit) |
---|
| 717 | _str += " Y-axis: %s\t[%s]\n" % (self._yaxis, self._yunit) |
---|
| 718 | _str += " Length: %g\n" % len(self.x) |
---|
| 719 | return _str |
---|
| 720 | |
---|
[4026380] | 721 | def is_slit_smeared(self): |
---|
| 722 | """ |
---|
[0997158f] | 723 | Check whether the data has slit smearing information |
---|
| 724 | :return: True is slit smearing info is present, False otherwise |
---|
[4026380] | 725 | """ |
---|
[f60a8c2] | 726 | def _check(v): |
---|
[a7a5886] | 727 | if (v.__class__ == list or v.__class__ == numpy.ndarray) \ |
---|
| 728 | and len(v) > 0 and min(v) > 0: |
---|
[4026380] | 729 | return True |
---|
| 730 | return False |
---|
| 731 | return _check(self.dxl) or _check(self.dxw) |
---|
[e4f421c] | 732 | |
---|
[7d8094b] | 733 | def clone_without_data(self, length=0, clone=None): |
---|
[b39c817] | 734 | """ |
---|
[0997158f] | 735 | Clone the current object, without copying the data (which |
---|
| 736 | will be filled out by a subsequent operation). |
---|
| 737 | The data arrays will be initialized to zero. |
---|
[e4f421c] | 738 | |
---|
[0997158f] | 739 | :param length: length of the data array to be initialized |
---|
| 740 | :param clone: if provided, the data will be copied to clone |
---|
[b39c817] | 741 | """ |
---|
[9198b83] | 742 | from copy import deepcopy |
---|
[e4f421c] | 743 | |
---|
[7d8094b] | 744 | if clone is None or not issubclass(clone.__class__, Data1D): |
---|
[e4f421c] | 745 | x = numpy.zeros(length) |
---|
[f60a8c2] | 746 | dx = numpy.zeros(length) |
---|
[e4f421c] | 747 | y = numpy.zeros(length) |
---|
[f60a8c2] | 748 | dy = numpy.zeros(length) |
---|
[a9f579c] | 749 | lam = numpy.zeros(length) |
---|
| 750 | dlam = numpy.zeros(length) |
---|
| 751 | clone = Data1D(x, y, lam=lam, dx=dx, dy=dy, dlam=dlam) |
---|
[e4f421c] | 752 | |
---|
| 753 | clone.title = self.title |
---|
| 754 | clone.run = self.run |
---|
| 755 | clone.filename = self.filename |
---|
| 756 | clone.instrument = self.instrument |
---|
| 757 | clone.notes = deepcopy(self.notes) |
---|
| 758 | clone.process = deepcopy(self.process) |
---|
| 759 | clone.detector = deepcopy(self.detector) |
---|
| 760 | clone.sample = deepcopy(self.sample) |
---|
| 761 | clone.source = deepcopy(self.source) |
---|
| 762 | clone.collimation = deepcopy(self.collimation) |
---|
[76cd1ae] | 763 | clone.trans_spectrum = deepcopy(self.trans_spectrum) |
---|
[e4f421c] | 764 | clone.meta_data = deepcopy(self.meta_data) |
---|
| 765 | clone.errors = deepcopy(self.errors) |
---|
| 766 | |
---|
[9198b83] | 767 | return clone |
---|
| 768 | |
---|
| 769 | def _validity_check(self, other): |
---|
| 770 | """ |
---|
[0997158f] | 771 | Checks that the data lengths are compatible. |
---|
| 772 | Checks that the x vectors are compatible. |
---|
| 773 | Returns errors vectors equal to original |
---|
| 774 | errors vectors if they were present or vectors |
---|
| 775 | of zeros when none was found. |
---|
[e4f421c] | 776 | |
---|
[0997158f] | 777 | :param other: other data set for operation |
---|
| 778 | :return: dy for self, dy for other [numpy arrays] |
---|
| 779 | :raise ValueError: when lengths are not compatible |
---|
[9198b83] | 780 | """ |
---|
| 781 | dy_other = None |
---|
| 782 | if isinstance(other, Data1D): |
---|
| 783 | # Check that data lengths are the same |
---|
| 784 | if len(self.x) != len(other.x) or \ |
---|
| 785 | len(self.y) != len(other.y): |
---|
[f60a8c2] | 786 | msg = "Unable to perform operation: data length are not equal" |
---|
[a7a5886] | 787 | raise ValueError, msg |
---|
[9198b83] | 788 | # Here we could also extrapolate between data points |
---|
[1b1a1c1] | 789 | TOLERANCE = 0.01 |
---|
[9198b83] | 790 | for i in range(len(self.x)): |
---|
[1b1a1c1] | 791 | if math.fabs((self.x[i] - other.x[i])/self.x[i]) > TOLERANCE: |
---|
[a7a5886] | 792 | msg = "Incompatible data sets: x-values do not match" |
---|
| 793 | raise ValueError, msg |
---|
[e4f421c] | 794 | |
---|
[9198b83] | 795 | # Check that the other data set has errors, otherwise |
---|
| 796 | # create zero vector |
---|
| 797 | dy_other = other.dy |
---|
[a7a5886] | 798 | if other.dy == None or (len(other.dy) != len(other.y)): |
---|
[9198b83] | 799 | dy_other = numpy.zeros(len(other.y)) |
---|
[e4f421c] | 800 | |
---|
[9198b83] | 801 | # Check that we have errors, otherwise create zero vector |
---|
| 802 | dy = self.dy |
---|
[a7a5886] | 803 | if self.dy == None or (len(self.dy) != len(self.y)): |
---|
[f60a8c2] | 804 | dy = numpy.zeros(len(self.y)) |
---|
[e4f421c] | 805 | |
---|
[9198b83] | 806 | return dy, dy_other |
---|
[a3084ada] | 807 | |
---|
[9198b83] | 808 | def _perform_operation(self, other, operation): |
---|
| 809 | """ |
---|
| 810 | """ |
---|
| 811 | # First, check the data compatibility |
---|
| 812 | dy, dy_other = self._validity_check(other) |
---|
| 813 | result = self.clone_without_data(len(self.x)) |
---|
[e2605a5] | 814 | if self.dxw == None: |
---|
| 815 | result.dxw = None |
---|
| 816 | else: |
---|
| 817 | result.dxw = numpy.zeros(len(self.x)) |
---|
| 818 | if self.dxl == None: |
---|
| 819 | result.dxl = None |
---|
| 820 | else: |
---|
| 821 | result.dxl = numpy.zeros(len(self.x)) |
---|
| 822 | |
---|
[9198b83] | 823 | for i in range(len(self.x)): |
---|
| 824 | result.x[i] = self.x[i] |
---|
[a7a5886] | 825 | if self.dx is not None and len(self.x) == len(self.dx): |
---|
[9198b83] | 826 | result.dx[i] = self.dx[i] |
---|
[e2605a5] | 827 | if self.dxw is not None and len(self.x) == len(self.dxw): |
---|
| 828 | result.dxw[i] = self.dxw[i] |
---|
| 829 | if self.dxl is not None and len(self.x) == len(self.dxl): |
---|
| 830 | result.dxl[i] = self.dxl[i] |
---|
[e4f421c] | 831 | |
---|
[9198b83] | 832 | a = Uncertainty(self.y[i], dy[i]**2) |
---|
| 833 | if isinstance(other, Data1D): |
---|
| 834 | b = Uncertainty(other.y[i], dy_other[i]**2) |
---|
[e2605a5] | 835 | if other.dx is not None: |
---|
| 836 | result.dx[i] *= self.dx[i] |
---|
| 837 | result.dx[i] += (other.dx[i]**2) |
---|
| 838 | result.dx[i] /= 2 |
---|
| 839 | result.dx[i] = math.sqrt(result.dx[i]) |
---|
| 840 | if result.dxl is not None and other.dxl is not None: |
---|
| 841 | result.dxl[i] *= self.dxl[i] |
---|
[a48842a2] | 842 | result.dxl[i] += (other.dxl[i]**2) |
---|
[e2605a5] | 843 | result.dxl[i] /= 2 |
---|
| 844 | result.dxl[i] = math.sqrt(result.dxl[i]) |
---|
[9198b83] | 845 | else: |
---|
| 846 | b = other |
---|
[e4f421c] | 847 | |
---|
[9198b83] | 848 | output = operation(a, b) |
---|
| 849 | result.y[i] = output.x |
---|
| 850 | result.dy[i] = math.sqrt(math.fabs(output.variance)) |
---|
| 851 | return result |
---|
[e4f421c] | 852 | |
---|
[a48842a2] | 853 | def _validity_check_union(self, other): |
---|
| 854 | """ |
---|
| 855 | Checks that the data lengths are compatible. |
---|
| 856 | Checks that the x vectors are compatible. |
---|
| 857 | Returns errors vectors equal to original |
---|
| 858 | errors vectors if they were present or vectors |
---|
| 859 | of zeros when none was found. |
---|
[e4f421c] | 860 | |
---|
[a48842a2] | 861 | :param other: other data set for operation |
---|
| 862 | :return: bool |
---|
| 863 | :raise ValueError: when data types are not compatible |
---|
| 864 | """ |
---|
| 865 | if not isinstance(other, Data1D): |
---|
| 866 | msg = "Unable to perform operation: different types of data set" |
---|
[e4f421c] | 867 | raise ValueError, msg |
---|
[a48842a2] | 868 | return True |
---|
| 869 | |
---|
| 870 | def _perform_union(self, other): |
---|
| 871 | """ |
---|
| 872 | """ |
---|
| 873 | # First, check the data compatibility |
---|
| 874 | self._validity_check_union(other) |
---|
| 875 | result = self.clone_without_data(len(self.x) + len(other.x)) |
---|
| 876 | if self.dy == None or other.dy is None: |
---|
| 877 | result.dy = None |
---|
| 878 | else: |
---|
| 879 | result.dy = numpy.zeros(len(self.x) + len(other.x)) |
---|
| 880 | if self.dx == None or other.dx is None: |
---|
| 881 | result.dx = None |
---|
| 882 | else: |
---|
| 883 | result.dx = numpy.zeros(len(self.x) + len(other.x)) |
---|
| 884 | if self.dxw == None or other.dxw is None: |
---|
| 885 | result.dxw = None |
---|
| 886 | else: |
---|
| 887 | result.dxw = numpy.zeros(len(self.x) + len(other.x)) |
---|
| 888 | if self.dxl == None or other.dxl is None: |
---|
| 889 | result.dxl = None |
---|
| 890 | else: |
---|
| 891 | result.dxl = numpy.zeros(len(self.x) + len(other.x)) |
---|
| 892 | |
---|
| 893 | result.x = numpy.append(self.x, other.x) |
---|
| 894 | #argsorting |
---|
| 895 | ind = numpy.argsort(result.x) |
---|
| 896 | result.x = result.x[ind] |
---|
| 897 | result.y = numpy.append(self.y, other.y) |
---|
| 898 | result.y = result.y[ind] |
---|
| 899 | if result.dy != None: |
---|
| 900 | result.dy = numpy.append(self.dy, other.dy) |
---|
| 901 | result.dy = result.dy[ind] |
---|
| 902 | if result.dx is not None: |
---|
| 903 | result.dx = numpy.append(self.dx, other.dx) |
---|
| 904 | result.dx = result.dx[ind] |
---|
| 905 | if result.dxw is not None: |
---|
| 906 | result.dxw = numpy.append(self.dxw, other.dxw) |
---|
| 907 | result.dxw = result.dxw[ind] |
---|
| 908 | if result.dxl is not None: |
---|
| 909 | result.dxl = numpy.append(self.dxl, other.dxl) |
---|
| 910 | result.dxl = result.dxl[ind] |
---|
| 911 | return result |
---|
[e4f421c] | 912 | |
---|
| 913 | |
---|
[7eaf9f2] | 914 | class Data2D(plottable_2D, DataInfo): |
---|
[99d1af6] | 915 | """ |
---|
[0997158f] | 916 | 2D data class |
---|
[99d1af6] | 917 | """ |
---|
| 918 | ## Units for Q-values |
---|
[ca10d8e] | 919 | Q_unit = '1/A' |
---|
[99d1af6] | 920 | ## Units for I(Q) values |
---|
[ca10d8e] | 921 | I_unit = '1/cm' |
---|
[99d1af6] | 922 | ## Vector of Q-values at the center of each bin in x |
---|
[d6513cd] | 923 | x_bins = None |
---|
[99d1af6] | 924 | ## Vector of Q-values at the center of each bin in y |
---|
[d6513cd] | 925 | y_bins = None |
---|
[e4f421c] | 926 | |
---|
[a7a5886] | 927 | def __init__(self, data=None, err_data=None, qx_data=None, |
---|
[f60a8c2] | 928 | qy_data=None, q_data=None, mask=None, |
---|
| 929 | dqx_data=None, dqy_data=None): |
---|
[d6513cd] | 930 | self.y_bins = [] |
---|
| 931 | self.x_bins = [] |
---|
[b99ac227] | 932 | DataInfo.__init__(self) |
---|
[a7a5886] | 933 | plottable_2D.__init__(self, data, err_data, qx_data, |
---|
[f60a8c2] | 934 | qy_data, q_data, mask, dqx_data, dqy_data) |
---|
[a7a5886] | 935 | if len(self.detector) > 0: |
---|
[b99ac227] | 936 | raise RuntimeError, "Data2D: Detector bank already filled at init" |
---|
[99d1af6] | 937 | |
---|
| 938 | def __str__(self): |
---|
[f60a8c2] | 939 | _str = "%s\n" % DataInfo.__str__(self) |
---|
[99d1af6] | 940 | _str += "Data:\n" |
---|
| 941 | _str += " Type: %s\n" % self.__class__.__name__ |
---|
| 942 | _str += " X- & Y-axis: %s\t[%s]\n" % (self._yaxis, self._yunit) |
---|
| 943 | _str += " Z-axis: %s\t[%s]\n" % (self._zaxis, self._zunit) |
---|
[3cd95c8] | 944 | _str += " Length: %g \n" % (len(self.data)) |
---|
[45d7662] | 945 | _str += " Shape: (%d, %d)\n" % (len(self.y_bins), len(self.x_bins)) |
---|
[99d1af6] | 946 | return _str |
---|
[e4f421c] | 947 | |
---|
[7d8094b] | 948 | def clone_without_data(self, length=0, clone=None): |
---|
[442f42f] | 949 | """ |
---|
[0997158f] | 950 | Clone the current object, without copying the data (which |
---|
| 951 | will be filled out by a subsequent operation). |
---|
| 952 | The data arrays will be initialized to zero. |
---|
[e4f421c] | 953 | |
---|
[0997158f] | 954 | :param length: length of the data array to be initialized |
---|
| 955 | :param clone: if provided, the data will be copied to clone |
---|
[442f42f] | 956 | """ |
---|
| 957 | from copy import deepcopy |
---|
[e4f421c] | 958 | |
---|
[f60a8c2] | 959 | if clone is None or not issubclass(clone.__class__, Data2D): |
---|
| 960 | data = numpy.zeros(length) |
---|
| 961 | err_data = numpy.zeros(length) |
---|
[3cd95c8] | 962 | qx_data = numpy.zeros(length) |
---|
| 963 | qy_data = numpy.zeros(length) |
---|
| 964 | q_data = numpy.zeros(length) |
---|
| 965 | mask = numpy.zeros(length) |
---|
| 966 | dqx_data = None |
---|
| 967 | dqy_data = None |
---|
[e4f421c] | 968 | clone = Data2D(data=data, err_data=err_data, |
---|
| 969 | qx_data=qx_data, qy_data=qy_data, |
---|
[0008f54] | 970 | q_data=q_data, mask=mask) |
---|
[3cd95c8] | 971 | |
---|
[e4f421c] | 972 | clone.title = self.title |
---|
| 973 | clone.run = self.run |
---|
| 974 | clone.filename = self.filename |
---|
| 975 | clone.instrument = self.instrument |
---|
| 976 | clone.notes = deepcopy(self.notes) |
---|
| 977 | clone.process = deepcopy(self.process) |
---|
| 978 | clone.detector = deepcopy(self.detector) |
---|
| 979 | clone.sample = deepcopy(self.sample) |
---|
| 980 | clone.source = deepcopy(self.source) |
---|
[f60a8c2] | 981 | clone.collimation = deepcopy(self.collimation) |
---|
[d72567e] | 982 | clone.trans_spectrum = deepcopy(self.trans_spectrum) |
---|
[e4f421c] | 983 | clone.meta_data = deepcopy(self.meta_data) |
---|
| 984 | clone.errors = deepcopy(self.errors) |
---|
| 985 | |
---|
[442f42f] | 986 | return clone |
---|
[e4f421c] | 987 | |
---|
[442f42f] | 988 | def _validity_check(self, other): |
---|
| 989 | """ |
---|
[0997158f] | 990 | Checks that the data lengths are compatible. |
---|
| 991 | Checks that the x vectors are compatible. |
---|
| 992 | Returns errors vectors equal to original |
---|
| 993 | errors vectors if they were present or vectors |
---|
| 994 | of zeros when none was found. |
---|
[e4f421c] | 995 | |
---|
[0997158f] | 996 | :param other: other data set for operation |
---|
| 997 | :return: dy for self, dy for other [numpy arrays] |
---|
| 998 | :raise ValueError: when lengths are not compatible |
---|
[442f42f] | 999 | """ |
---|
| 1000 | err_other = None |
---|
[1b1a1c1] | 1001 | TOLERANCE = 0.01 |
---|
[442f42f] | 1002 | if isinstance(other, Data2D): |
---|
| 1003 | # Check that data lengths are the same |
---|
[dcf73a4] | 1004 | if len(self.data) != len(other.data) or \ |
---|
| 1005 | len(self.qx_data) != len(other.qx_data) or \ |
---|
| 1006 | len(self.qy_data) != len(other.qy_data): |
---|
[a7a5886] | 1007 | msg = "Unable to perform operation: data length are not equal" |
---|
| 1008 | raise ValueError, msg |
---|
[dcf73a4] | 1009 | for ind in range(len(self.data)): |
---|
[1b1a1c1] | 1010 | if math.fabs((self.qx_data[ind] - other.qx_data[ind])/self.qx_data[ind]) > TOLERANCE: |
---|
| 1011 | msg = "Incompatible data sets: qx-values do not match: %s %s" % (self.qx_data[ind], other.qx_data[ind]) |
---|
[dcf73a4] | 1012 | raise ValueError, msg |
---|
[1b1a1c1] | 1013 | if math.fabs((self.qy_data[ind] - other.qy_data[ind])/self.qy_data[ind]) > TOLERANCE: |
---|
| 1014 | msg = "Incompatible data sets: qy-values do not match: %s %s" % (self.qy_data[ind], other.qy_data[ind]) |
---|
[dcf73a4] | 1015 | raise ValueError, msg |
---|
[e4f421c] | 1016 | |
---|
[442f42f] | 1017 | # Check that the scales match |
---|
| 1018 | err_other = other.err_data |
---|
[a7a5886] | 1019 | if other.err_data == None or \ |
---|
[dcf73a4] | 1020 | (len(other.err_data) != len(other.data)): |
---|
| 1021 | err_other = numpy.zeros(len(other.data)) |
---|
[e4f421c] | 1022 | |
---|
[442f42f] | 1023 | # Check that we have errors, otherwise create zero vector |
---|
| 1024 | err = self.err_data |
---|
[a7a5886] | 1025 | if self.err_data == None or \ |
---|
[dcf73a4] | 1026 | (len(self.err_data) != len(self.data)): |
---|
| 1027 | err = numpy.zeros(len(other.data)) |
---|
[442f42f] | 1028 | return err, err_other |
---|
[e4f421c] | 1029 | |
---|
[442f42f] | 1030 | def _perform_operation(self, other, operation): |
---|
| 1031 | """ |
---|
[0997158f] | 1032 | Perform 2D operations between data sets |
---|
[e4f421c] | 1033 | |
---|
[0997158f] | 1034 | :param other: other data set |
---|
| 1035 | :param operation: function defining the operation |
---|
[442f42f] | 1036 | """ |
---|
| 1037 | # First, check the data compatibility |
---|
| 1038 | dy, dy_other = self._validity_check(other) |
---|
[e2605a5] | 1039 | result = self.clone_without_data(numpy.size(self.data)) |
---|
| 1040 | if self.dqx_data == None or self.dqy_data == None: |
---|
| 1041 | result.dqx_data = None |
---|
| 1042 | result.dqy_data = None |
---|
| 1043 | else: |
---|
[cdeed9f] | 1044 | result.dqx_data = numpy.zeros(len(self.data)) |
---|
| 1045 | result.dqy_data = numpy.zeros(len(self.data)) |
---|
[e2605a5] | 1046 | for i in range(numpy.size(self.data)): |
---|
[cdeed9f] | 1047 | result.data[i] = self.data[i] |
---|
| 1048 | if self.err_data is not None and \ |
---|
| 1049 | numpy.size(self.data) == numpy.size(self.err_data): |
---|
[e4f421c] | 1050 | result.err_data[i] = self.err_data[i] |
---|
[cdeed9f] | 1051 | if self.dqx_data is not None: |
---|
| 1052 | result.dqx_data[i] = self.dqx_data[i] |
---|
| 1053 | if self.dqy_data is not None: |
---|
| 1054 | result.dqy_data[i] = self.dqy_data[i] |
---|
| 1055 | result.qx_data[i] = self.qx_data[i] |
---|
| 1056 | result.qy_data[i] = self.qy_data[i] |
---|
| 1057 | result.q_data[i] = self.q_data[i] |
---|
| 1058 | result.mask[i] = self.mask[i] |
---|
[e4f421c] | 1059 | |
---|
[e2605a5] | 1060 | a = Uncertainty(self.data[i], dy[i]**2) |
---|
| 1061 | if isinstance(other, Data2D): |
---|
| 1062 | b = Uncertainty(other.data[i], dy_other[i]**2) |
---|
| 1063 | if other.dqx_data is not None and \ |
---|
| 1064 | result.dqx_data is not None: |
---|
| 1065 | result.dqx_data[i] *= self.dqx_data[i] |
---|
| 1066 | result.dqx_data[i] += (other.dqx_data[i]**2) |
---|
| 1067 | result.dqx_data[i] /= 2 |
---|
[e4f421c] | 1068 | result.dqx_data[i] = math.sqrt(result.dqx_data[i]) |
---|
[e2605a5] | 1069 | if other.dqy_data is not None and \ |
---|
| 1070 | result.dqy_data is not None: |
---|
| 1071 | result.dqy_data[i] *= self.dqy_data[i] |
---|
| 1072 | result.dqy_data[i] += (other.dqy_data[i]**2) |
---|
| 1073 | result.dqy_data[i] /= 2 |
---|
| 1074 | result.dqy_data[i] = math.sqrt(result.dqy_data[i]) |
---|
| 1075 | else: |
---|
| 1076 | b = other |
---|
| 1077 | output = operation(a, b) |
---|
| 1078 | result.data[i] = output.x |
---|
| 1079 | result.err_data[i] = math.sqrt(math.fabs(output.variance)) |
---|
[442f42f] | 1080 | return result |
---|
[e4f421c] | 1081 | |
---|
[a48842a2] | 1082 | def _validity_check_union(self, other): |
---|
| 1083 | """ |
---|
| 1084 | Checks that the data lengths are compatible. |
---|
| 1085 | Checks that the x vectors are compatible. |
---|
| 1086 | Returns errors vectors equal to original |
---|
| 1087 | errors vectors if they were present or vectors |
---|
| 1088 | of zeros when none was found. |
---|
[e4f421c] | 1089 | |
---|
[a48842a2] | 1090 | :param other: other data set for operation |
---|
| 1091 | :return: bool |
---|
| 1092 | :raise ValueError: when data types are not compatible |
---|
| 1093 | """ |
---|
| 1094 | if not isinstance(other, Data2D): |
---|
| 1095 | msg = "Unable to perform operation: different types of data set" |
---|
[e4f421c] | 1096 | raise ValueError, msg |
---|
[a48842a2] | 1097 | return True |
---|
[e4f421c] | 1098 | |
---|
[a48842a2] | 1099 | def _perform_union(self, other): |
---|
| 1100 | """ |
---|
| 1101 | Perform 2D operations between data sets |
---|
[e4f421c] | 1102 | |
---|
[a48842a2] | 1103 | :param other: other data set |
---|
| 1104 | :param operation: function defining the operation |
---|
| 1105 | """ |
---|
| 1106 | # First, check the data compatibility |
---|
| 1107 | self._validity_check_union(other) |
---|
| 1108 | result = self.clone_without_data(numpy.size(self.data) + \ |
---|
| 1109 | numpy.size(other.data)) |
---|
| 1110 | result.xmin = self.xmin |
---|
| 1111 | result.xmax = self.xmax |
---|
| 1112 | result.ymin = self.ymin |
---|
| 1113 | result.ymax = self.ymax |
---|
| 1114 | if self.dqx_data == None or self.dqy_data == None or \ |
---|
[e4f421c] | 1115 | other.dqx_data == None or other.dqy_data == None: |
---|
[a48842a2] | 1116 | result.dqx_data = None |
---|
| 1117 | result.dqy_data = None |
---|
| 1118 | else: |
---|
| 1119 | result.dqx_data = numpy.zeros(len(self.data) + \ |
---|
| 1120 | numpy.size(other.data)) |
---|
| 1121 | result.dqy_data = numpy.zeros(len(self.data) + \ |
---|
| 1122 | numpy.size(other.data)) |
---|
[e4f421c] | 1123 | |
---|
[a48842a2] | 1124 | result.data = numpy.append(self.data, other.data) |
---|
| 1125 | result.qx_data = numpy.append(self.qx_data, other.qx_data) |
---|
| 1126 | result.qy_data = numpy.append(self.qy_data, other.qy_data) |
---|
| 1127 | result.q_data = numpy.append(self.q_data, other.q_data) |
---|
| 1128 | result.mask = numpy.append(self.mask, other.mask) |
---|
| 1129 | if result.err_data is not None: |
---|
[a4deca6] | 1130 | result.err_data = numpy.append(self.err_data, other.err_data) |
---|
[a48842a2] | 1131 | if self.dqx_data is not None: |
---|
| 1132 | result.dqx_data = numpy.append(self.dqx_data, other.dqx_data) |
---|
| 1133 | if self.dqy_data is not None: |
---|
| 1134 | result.dqy_data = numpy.append(self.dqy_data, other.dqy_data) |
---|
| 1135 | |
---|
| 1136 | return result |
---|
[d72567e] | 1137 | |
---|
| 1138 | |
---|
| 1139 | def combine_data_info_with_plottable(data, datainfo): |
---|
| 1140 | """ |
---|
| 1141 | A function that combines the DataInfo data in self.current_datainto with a plottable_1D or 2D data object. |
---|
| 1142 | |
---|
| 1143 | :param data: A plottable_1D or plottable_2D data object |
---|
| 1144 | :return: A fully specified Data1D or Data2D object |
---|
| 1145 | """ |
---|
| 1146 | |
---|
| 1147 | final_dataset = None |
---|
| 1148 | if isinstance(data, plottable_1D): |
---|
| 1149 | final_dataset = Data1D(data.x, data.y) |
---|
| 1150 | final_dataset.dx = data.dx |
---|
| 1151 | final_dataset.dy = data.dy |
---|
| 1152 | final_dataset.dxl = data.dxl |
---|
| 1153 | final_dataset.dxw = data.dxw |
---|
| 1154 | final_dataset.xaxis(data._xaxis, data._xunit) |
---|
| 1155 | final_dataset.yaxis(data._yaxis, data._yunit) |
---|
| 1156 | elif isinstance(data, plottable_2D): |
---|
| 1157 | final_dataset = Data2D(data.data, data.err_data, data.qx_data, data.qy_data, data.q_data, |
---|
| 1158 | data.mask, data.dqx_data, data.dqy_data) |
---|
| 1159 | final_dataset.xaxis(data._xaxis, data._xunit) |
---|
| 1160 | final_dataset.yaxis(data._yaxis, data._yunit) |
---|
| 1161 | final_dataset.zaxis(data._zaxis, data._zunit) |
---|
[a4deca6] | 1162 | final_dataset.x_bins = data.x_bins |
---|
| 1163 | final_dataset.y_bins = data.y_bins |
---|
[d72567e] | 1164 | else: |
---|
| 1165 | return_string = "Should Never Happen: _combine_data_info_with_plottable input is not a plottable1d or " + \ |
---|
| 1166 | "plottable2d data object" |
---|
| 1167 | return return_string |
---|
| 1168 | |
---|
| 1169 | final_dataset.xmax = data.xmax |
---|
| 1170 | final_dataset.ymax = data.ymax |
---|
| 1171 | final_dataset.xmin = data.xmin |
---|
| 1172 | final_dataset.ymin = data.ymin |
---|
| 1173 | final_dataset.title = datainfo.title |
---|
| 1174 | final_dataset.run = datainfo.run |
---|
| 1175 | final_dataset.run_name = datainfo.run_name |
---|
| 1176 | final_dataset.filename = datainfo.filename |
---|
| 1177 | final_dataset.notes = datainfo.notes |
---|
| 1178 | final_dataset.process = datainfo.process |
---|
| 1179 | final_dataset.instrument = datainfo.instrument |
---|
| 1180 | final_dataset.detector = datainfo.detector |
---|
| 1181 | final_dataset.sample = datainfo.sample |
---|
| 1182 | final_dataset.source = datainfo.source |
---|
| 1183 | final_dataset.collimation = datainfo.collimation |
---|
| 1184 | final_dataset.trans_spectrum = datainfo.trans_spectrum |
---|
| 1185 | final_dataset.meta_data = datainfo.meta_data |
---|
| 1186 | final_dataset.errors = datainfo.errors |
---|
[a4deca6] | 1187 | return final_dataset |
---|