| 1 | """ |
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| 2 | Module that contains classes to hold information read from |
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| 3 | reduced data files. |
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| 4 | |
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| 5 | A good description of the data members can be found in |
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| 6 | the CanSAS 1D XML data format: |
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| 7 | |
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| 8 | http://www.smallangles.net/wgwiki/index.php/cansas1d_documentation |
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| 9 | """ |
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| 10 | ##################################################################### |
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| 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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| 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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| 15 | #copyright 2008, University of Tennessee |
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| 16 | ###################################################################### |
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| 17 | |
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| 18 | |
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| 19 | #TODO: Keep track of data manipulation in the 'process' data structure. |
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| 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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| 22 | |
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| 23 | #from sans.guitools.plottables import Data1D as plottable_1D |
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| 24 | from data_util.uncertainty import Uncertainty |
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| 25 | import numpy |
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| 26 | import math |
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| 27 | |
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| 28 | |
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| 29 | class plottable_1D: |
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| 30 | """ |
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| 31 | Data1D is a place holder for 1D plottables. |
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| 32 | """ |
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| 33 | # The presence of these should be mutually |
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| 34 | # exclusive with the presence of Qdev (dx) |
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| 35 | x = None |
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| 36 | y = None |
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| 37 | dx = None |
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| 38 | dy = None |
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| 39 | ## Slit smearing length |
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| 40 | dxl = None |
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| 41 | ## Slit smearing width |
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| 42 | dxw = None |
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| 43 | |
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| 44 | # Units |
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| 45 | _xaxis = '' |
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| 46 | _xunit = '' |
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| 47 | _yaxis = '' |
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| 48 | _yunit = '' |
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| 49 | |
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| 50 | def __init__(self, x, y, dx=None, dy=None, dxl=None, dxw=None): |
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| 51 | self.x = numpy.asarray(x) |
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| 52 | self.y = numpy.asarray(y) |
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| 53 | if dx is not None: |
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| 54 | self.dx = numpy.asarray(dx) |
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| 55 | if dy is not None: |
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| 56 | self.dy = numpy.asarray(dy) |
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| 57 | if dxl is not None: |
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| 58 | self.dxl = numpy.asarray(dxl) |
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| 59 | if dxw is not None: |
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| 60 | self.dxw = numpy.asarray(dxw) |
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| 61 | |
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| 62 | def xaxis(self, label, unit): |
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| 63 | """ |
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| 64 | set the x axis label and unit |
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| 65 | """ |
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| 66 | self._xaxis = label |
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| 67 | self._xunit = unit |
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| 68 | |
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| 69 | def yaxis(self, label, unit): |
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| 70 | """ |
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| 71 | set the y axis label and unit |
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| 72 | """ |
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| 73 | self._yaxis = label |
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| 74 | self._yunit = unit |
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| 75 | |
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| 76 | |
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| 77 | class plottable_2D: |
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| 78 | """ |
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| 79 | Data2D is a place holder for 2D plottables. |
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| 80 | """ |
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| 81 | xmin = None |
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| 82 | xmax = None |
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| 83 | ymin = None |
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| 84 | ymax = None |
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| 85 | data = None |
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| 86 | qx_data = None |
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| 87 | qy_data = None |
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| 88 | q_data = None |
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| 89 | err_data = None |
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| 90 | dqx_data = None |
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| 91 | dqy_data = None |
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| 92 | mask = None |
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| 93 | |
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| 94 | # Units |
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| 95 | _xaxis = '' |
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| 96 | _xunit = '' |
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| 97 | _yaxis = '' |
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| 98 | _yunit = '' |
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| 99 | _zaxis = '' |
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| 100 | _zunit = '' |
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| 101 | |
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| 102 | def __init__(self, data=None, err_data=None, qx_data=None, |
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| 103 | qy_data=None, q_data=None, mask=None, |
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| 104 | dqx_data=None, dqy_data=None): |
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| 105 | self.data = numpy.asarray(data) |
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| 106 | self.qx_data = numpy.asarray(qx_data) |
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| 107 | self.qy_data = numpy.asarray(qy_data) |
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| 108 | self.q_data = numpy.asarray(q_data) |
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| 109 | self.mask = numpy.asarray(mask) |
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| 110 | self.err_data = numpy.asarray(err_data) |
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| 111 | if dqx_data is not None: |
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| 112 | self.dqx_data = numpy.asarray(dqx_data) |
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| 113 | if dqy_data is not None: |
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| 114 | self.dqy_data = numpy.asarray(dqy_data) |
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| 115 | |
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| 116 | def xaxis(self, label, unit): |
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| 117 | """ |
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| 118 | set the x axis label and unit |
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| 119 | """ |
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| 120 | self._xaxis = label |
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| 121 | self._xunit = unit |
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| 122 | |
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| 123 | def yaxis(self, label, unit): |
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| 124 | """ |
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| 125 | set the y axis label and unit |
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| 126 | """ |
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| 127 | self._yaxis = label |
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| 128 | self._yunit = unit |
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| 129 | |
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| 130 | def zaxis(self, label, unit): |
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| 131 | """ |
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| 132 | set the z axis label and unit |
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| 133 | """ |
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| 134 | self._zaxis = label |
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| 135 | self._zunit = unit |
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| 136 | |
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| 137 | |
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| 138 | class Vector: |
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| 139 | """ |
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| 140 | Vector class to hold multi-dimensional objects |
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| 141 | """ |
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| 142 | ## x component |
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| 143 | x = None |
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| 144 | ## y component |
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| 145 | y = None |
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| 146 | ## z component |
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| 147 | z = None |
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| 148 | |
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| 149 | def __init__(self, x=None, y=None, z=None): |
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| 150 | """ |
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| 151 | Initialization. Components that are not |
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| 152 | set a set to None by default. |
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| 153 | |
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| 154 | :param x: x component |
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| 155 | :param y: y component |
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| 156 | :param z: z component |
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| 157 | |
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| 158 | """ |
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| 159 | self.x = x |
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| 160 | self.y = y |
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| 161 | self.z = z |
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| 162 | |
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| 163 | def __str__(self): |
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| 164 | msg = "x = %s\ty = %s\tz = %s" % (str(self.x), str(self.y), str(self.z)) |
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| 165 | return msg |
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| 166 | |
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| 167 | |
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| 168 | class Detector: |
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| 169 | """ |
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| 170 | Class to hold detector information |
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| 171 | """ |
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| 172 | ## Name of the instrument [string] |
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| 173 | name = None |
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| 174 | ## Sample to detector distance [float] [mm] |
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| 175 | distance = None |
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| 176 | distance_unit = 'mm' |
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| 177 | ## Offset of this detector position in X, Y, |
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| 178 | #(and Z if necessary) [Vector] [mm] |
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| 179 | offset = None |
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| 180 | offset_unit = 'm' |
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| 181 | ## Orientation (rotation) of this detector in roll, |
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| 182 | # pitch, and yaw [Vector] [degrees] |
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| 183 | orientation = None |
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| 184 | orientation_unit = 'degree' |
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| 185 | ## Center of the beam on the detector in X and Y |
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| 186 | #(and Z if necessary) [Vector] [mm] |
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| 187 | beam_center = None |
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| 188 | beam_center_unit = 'mm' |
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| 189 | ## Pixel size in X, Y, (and Z if necessary) [Vector] [mm] |
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| 190 | pixel_size = None |
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| 191 | pixel_size_unit = 'mm' |
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| 192 | ## Slit length of the instrument for this detector.[float] [mm] |
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| 193 | slit_length = None |
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| 194 | slit_length_unit = 'mm' |
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| 195 | |
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| 196 | def __init__(self): |
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| 197 | """ |
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| 198 | |
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| 199 | Initialize class attribute that are objects... |
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| 200 | |
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| 201 | """ |
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| 202 | self.offset = Vector() |
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| 203 | self.orientation = Vector() |
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| 204 | self.beam_center = Vector() |
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| 205 | self.pixel_size = Vector() |
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| 206 | |
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| 207 | def __str__(self): |
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| 208 | _str = "Detector:\n" |
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| 209 | _str += " Name: %s\n" % self.name |
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| 210 | _str += " Distance: %s [%s]\n" % \ |
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| 211 | (str(self.distance), str(self.distance_unit)) |
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| 212 | _str += " Offset: %s [%s]\n" % \ |
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| 213 | (str(self.offset), str(self.offset_unit)) |
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| 214 | _str += " Orientation: %s [%s]\n" % \ |
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| 215 | (str(self.orientation), str(self.orientation_unit)) |
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| 216 | _str += " Beam center: %s [%s]\n" % \ |
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| 217 | (str(self.beam_center), str(self.beam_center_unit)) |
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| 218 | _str += " Pixel size: %s [%s]\n" % \ |
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| 219 | (str(self.pixel_size), str(self.pixel_size_unit)) |
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| 220 | _str += " Slit length: %s [%s]\n" % \ |
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| 221 | (str(self.slit_length), str(self.slit_length_unit)) |
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| 222 | return _str |
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| 223 | |
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| 224 | |
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| 225 | class Aperture: |
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| 226 | ## Name |
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| 227 | name = None |
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| 228 | ## Type |
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| 229 | type = None |
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| 230 | ## Size name |
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| 231 | size_name = None |
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| 232 | ## Aperture size [Vector] |
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| 233 | size = None |
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| 234 | size_unit = 'mm' |
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| 235 | ## Aperture distance [float] |
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| 236 | distance = None |
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| 237 | distance_unit = 'mm' |
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| 238 | |
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| 239 | def __init__(self): |
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| 240 | self.size = Vector() |
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| 241 | |
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| 242 | |
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| 243 | class Collimation: |
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| 244 | """ |
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| 245 | Class to hold collimation information |
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| 246 | """ |
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| 247 | ## Name |
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| 248 | name = None |
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| 249 | ## Length [float] [mm] |
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| 250 | length = None |
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| 251 | length_unit = 'mm' |
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| 252 | ## Aperture |
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| 253 | aperture = None |
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| 254 | |
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| 255 | def __init__(self): |
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| 256 | self.aperture = [] |
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| 257 | |
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| 258 | def __str__(self): |
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| 259 | _str = "Collimation:\n" |
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| 260 | _str += " Length: %s [%s]\n" % \ |
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| 261 | (str(self.length), str(self.length_unit)) |
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| 262 | for item in self.aperture: |
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| 263 | _str += " Aperture size:%s [%s]\n" % \ |
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| 264 | (str(item.size), str(item.size_unit)) |
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| 265 | _str += " Aperture_dist:%s [%s]\n" % \ |
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| 266 | (str(item.distance), str(item.distance_unit)) |
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| 267 | return _str |
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| 268 | |
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| 269 | |
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| 270 | class Source: |
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| 271 | """ |
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| 272 | Class to hold source information |
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| 273 | """ |
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| 274 | ## Name |
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| 275 | name = None |
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| 276 | ## Radiation type [string] |
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| 277 | radiation = None |
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| 278 | ## Beam size name |
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| 279 | beam_size_name = None |
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| 280 | ## Beam size [Vector] [mm] |
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| 281 | beam_size = None |
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| 282 | beam_size_unit = 'mm' |
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| 283 | ## Beam shape [string] |
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| 284 | beam_shape = None |
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| 285 | ## Wavelength [float] [Angstrom] |
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| 286 | wavelength = None |
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| 287 | wavelength_unit = 'A' |
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| 288 | ## Minimum wavelength [float] [Angstrom] |
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| 289 | wavelength_min = None |
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| 290 | wavelength_min_unit = 'nm' |
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| 291 | ## Maximum wavelength [float] [Angstrom] |
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| 292 | wavelength_max = None |
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| 293 | wavelength_max_unit = 'nm' |
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| 294 | ## Wavelength spread [float] [Angstrom] |
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| 295 | wavelength_spread = None |
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| 296 | wavelength_spread_unit = 'percent' |
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| 297 | |
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| 298 | def __init__(self): |
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| 299 | self.beam_size = Vector() |
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| 300 | |
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| 301 | def __str__(self): |
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| 302 | _str = "Source:\n" |
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| 303 | _str += " Radiation: %s\n" % str(self.radiation) |
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| 304 | _str += " Shape: %s\n" % str(self.beam_shape) |
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| 305 | _str += " Wavelength: %s [%s]\n" % \ |
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| 306 | (str(self.wavelength), str(self.wavelength_unit)) |
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| 307 | _str += " Waveln_min: %s [%s]\n" % \ |
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| 308 | (str(self.wavelength_min), str(self.wavelength_min_unit)) |
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| 309 | _str += " Waveln_max: %s [%s]\n" % \ |
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| 310 | (str(self.wavelength_max), str(self.wavelength_max_unit)) |
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| 311 | _str += " Waveln_spread:%s [%s]\n" % \ |
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| 312 | (str(self.wavelength_spread), str(self.wavelength_spread_unit)) |
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| 313 | _str += " Beam_size: %s [%s]\n" % \ |
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| 314 | (str(self.beam_size), str(self.beam_size_unit)) |
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| 315 | return _str |
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| 316 | |
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| 317 | |
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| 318 | """ |
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| 319 | Definitions of radiation types |
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| 320 | """ |
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| 321 | NEUTRON = 'neutron' |
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| 322 | XRAY = 'x-ray' |
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| 323 | MUON = 'muon' |
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| 324 | ELECTRON = 'electron' |
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| 325 | |
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| 326 | |
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| 327 | class Sample: |
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| 328 | """ |
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| 329 | Class to hold the sample description |
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| 330 | """ |
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| 331 | ## Short name for sample |
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| 332 | name = '' |
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| 333 | ## ID |
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| 334 | ID = '' |
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| 335 | ## Thickness [float] [mm] |
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| 336 | thickness = None |
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| 337 | thickness_unit = 'mm' |
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| 338 | ## Transmission [float] [fraction] |
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| 339 | transmission = None |
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| 340 | ## Temperature [float] [C] |
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| 341 | temperature = None |
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| 342 | temperature_unit = 'C' |
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| 343 | ## Position [Vector] [mm] |
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| 344 | position = None |
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| 345 | position_unit = 'mm' |
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| 346 | ## Orientation [Vector] [degrees] |
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| 347 | orientation = None |
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| 348 | orientation_unit = 'degree' |
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| 349 | ## Details |
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| 350 | details = None |
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| 351 | |
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| 352 | def __init__(self): |
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| 353 | self.position = Vector() |
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| 354 | self.orientation = Vector() |
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| 355 | self.details = [] |
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| 356 | |
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| 357 | def __str__(self): |
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| 358 | _str = "Sample:\n" |
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| 359 | _str += " ID: %s\n" % str(self.ID) |
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| 360 | _str += " Transmission: %s\n" % str(self.transmission) |
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| 361 | _str += " Thickness: %s [%s]\n" % \ |
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| 362 | (str(self.thickness), str(self.thickness_unit)) |
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| 363 | _str += " Temperature: %s [%s]\n" % \ |
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| 364 | (str(self.temperature), str(self.temperature_unit)) |
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| 365 | _str += " Position: %s [%s]\n" % \ |
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| 366 | (str(self.position), str(self.position_unit)) |
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| 367 | _str += " Orientation: %s [%s]\n" % \ |
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| 368 | (str(self.orientation), str(self.orientation_unit)) |
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| 369 | |
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| 370 | _str += " Details:\n" |
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| 371 | for item in self.details: |
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| 372 | _str += " %s\n" % item |
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| 373 | |
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| 374 | return _str |
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| 375 | |
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| 376 | |
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| 377 | class Process: |
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| 378 | """ |
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| 379 | Class that holds information about the processes |
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| 380 | performed on the data. |
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| 381 | """ |
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| 382 | name = '' |
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| 383 | date = '' |
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| 384 | description = '' |
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| 385 | term = None |
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| 386 | notes = None |
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| 387 | |
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| 388 | def __init__(self): |
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| 389 | self.term = [] |
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| 390 | self.notes = [] |
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| 391 | |
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| 392 | def __str__(self): |
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| 393 | _str = "Process:\n" |
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| 394 | _str += " Name: %s\n" % self.name |
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| 395 | _str += " Date: %s\n" % self.date |
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| 396 | _str += " Description: %s\n" % self.description |
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| 397 | for item in self.term: |
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| 398 | _str += " Term: %s\n" % item |
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| 399 | for item in self.notes: |
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| 400 | _str += " Note: %s\n" % item |
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| 401 | return _str |
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| 402 | |
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| 403 | |
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| 404 | class DataInfo: |
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| 405 | """ |
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| 406 | Class to hold the data read from a file. |
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| 407 | It includes four blocks of data for the |
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| 408 | instrument description, the sample description, |
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| 409 | the data itself and any other meta data. |
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| 410 | """ |
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| 411 | ## Title |
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| 412 | title = '' |
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| 413 | ## Run number |
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| 414 | run = None |
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| 415 | ## Run name |
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| 416 | run_name = None |
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| 417 | ## File name |
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| 418 | filename = '' |
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| 419 | ## Notes |
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| 420 | notes = None |
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| 421 | ## Processes (Action on the data) |
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| 422 | process = None |
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| 423 | ## Instrument name |
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| 424 | instrument = '' |
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| 425 | ## Detector information |
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| 426 | detector = None |
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| 427 | ## Sample information |
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| 428 | sample = None |
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| 429 | ## Source information |
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| 430 | source = None |
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| 431 | ## Collimation information |
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| 432 | collimation = None |
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| 433 | ## Additional meta-data |
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| 434 | meta_data = None |
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| 435 | ## Loading errors |
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| 436 | errors = None |
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| 437 | |
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| 438 | def __init__(self): |
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| 439 | """ |
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| 440 | Initialization |
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| 441 | """ |
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| 442 | ## Title |
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| 443 | self.title = '' |
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| 444 | ## Run number |
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| 445 | self.run = [] |
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| 446 | self.run_name = {} |
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| 447 | ## File name |
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| 448 | self.filename = '' |
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| 449 | ## Notes |
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| 450 | self.notes = [] |
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| 451 | ## Processes (Action on the data) |
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| 452 | self.process = [] |
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| 453 | ## Instrument name |
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| 454 | self.instrument = '' |
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| 455 | ## Detector information |
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| 456 | self.detector = [] |
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| 457 | ## Sample information |
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| 458 | self.sample = Sample() |
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| 459 | ## Source information |
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| 460 | self.source = Source() |
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| 461 | ## Collimation information |
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| 462 | self.collimation = [] |
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| 463 | ## Additional meta-data |
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| 464 | self.meta_data = {} |
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| 465 | ## Loading errors |
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| 466 | self.errors = [] |
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| 467 | |
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| 468 | def append_empty_process(self): |
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| 469 | """ |
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| 470 | """ |
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| 471 | self.process.append(Process()) |
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| 472 | |
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| 473 | def add_notes(self, message=""): |
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| 474 | """ |
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| 475 | Add notes to datainfo |
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| 476 | """ |
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| 477 | self.notes.append(message) |
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| 478 | |
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| 479 | def __str__(self): |
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| 480 | """ |
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| 481 | Nice printout |
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| 482 | """ |
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| 483 | _str = "File: %s\n" % self.filename |
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| 484 | _str += "Title: %s\n" % self.title |
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| 485 | _str += "Run: %s\n" % str(self.run) |
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| 486 | _str += "Instrument: %s\n" % str(self.instrument) |
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| 487 | _str += "%s\n" % str(self.sample) |
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| 488 | _str += "%s\n" % str(self.source) |
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| 489 | for item in self.detector: |
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| 490 | _str += "%s\n" % str(item) |
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| 491 | for item in self.collimation: |
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| 492 | _str += "%s\n" % str(item) |
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| 493 | for item in self.process: |
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| 494 | _str += "%s\n" % str(item) |
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| 495 | for item in self.notes: |
|---|
| 496 | _str += "%s\n" % str(item) |
|---|
| 497 | |
|---|
| 498 | return _str |
|---|
| 499 | |
|---|
| 500 | # Private method to perform operation. Not implemented for DataInfo, |
|---|
| 501 | # but should be implemented for each data class inherited from DataInfo |
|---|
| 502 | # that holds actual data (ex.: Data1D) |
|---|
| 503 | def _perform_operation(self, other, operation): |
|---|
| 504 | """ |
|---|
| 505 | Private method to perform operation. Not implemented for DataInfo, |
|---|
| 506 | but should be implemented for each data class inherited from DataInfo |
|---|
| 507 | that holds actual data (ex.: Data1D) |
|---|
| 508 | """ |
|---|
| 509 | return NotImplemented |
|---|
| 510 | |
|---|
| 511 | def __add__(self, other): |
|---|
| 512 | """ |
|---|
| 513 | Add two data sets |
|---|
| 514 | |
|---|
| 515 | :param other: data set to add to the current one |
|---|
| 516 | :return: new data set |
|---|
| 517 | :raise ValueError: raised when two data sets are incompatible |
|---|
| 518 | """ |
|---|
| 519 | def operation(a, b): |
|---|
| 520 | return a + b |
|---|
| 521 | return self._perform_operation(other, operation) |
|---|
| 522 | |
|---|
| 523 | def __radd__(self, other): |
|---|
| 524 | """ |
|---|
| 525 | Add two data sets |
|---|
| 526 | |
|---|
| 527 | :param other: data set to add to the current one |
|---|
| 528 | |
|---|
| 529 | :return: new data set |
|---|
| 530 | |
|---|
| 531 | :raise ValueError: raised when two data sets are incompatible |
|---|
| 532 | |
|---|
| 533 | """ |
|---|
| 534 | def operation(a, b): |
|---|
| 535 | return b + a |
|---|
| 536 | return self._perform_operation(other, operation) |
|---|
| 537 | |
|---|
| 538 | def __sub__(self, other): |
|---|
| 539 | """ |
|---|
| 540 | Subtract two data sets |
|---|
| 541 | |
|---|
| 542 | :param other: data set to subtract from the current one |
|---|
| 543 | |
|---|
| 544 | :return: new data set |
|---|
| 545 | |
|---|
| 546 | :raise ValueError: raised when two data sets are incompatible |
|---|
| 547 | |
|---|
| 548 | """ |
|---|
| 549 | def operation(a, b): |
|---|
| 550 | return a - b |
|---|
| 551 | return self._perform_operation(other, operation) |
|---|
| 552 | |
|---|
| 553 | def __rsub__(self, other): |
|---|
| 554 | """ |
|---|
| 555 | Subtract two data sets |
|---|
| 556 | |
|---|
| 557 | :param other: data set to subtract from the current one |
|---|
| 558 | |
|---|
| 559 | :return: new data set |
|---|
| 560 | |
|---|
| 561 | :raise ValueError: raised when two data sets are incompatible |
|---|
| 562 | |
|---|
| 563 | """ |
|---|
| 564 | def operation(a, b): |
|---|
| 565 | return b - a |
|---|
| 566 | return self._perform_operation(other, operation) |
|---|
| 567 | |
|---|
| 568 | def __mul__(self, other): |
|---|
| 569 | """ |
|---|
| 570 | Multiply two data sets |
|---|
| 571 | |
|---|
| 572 | :param other: data set to subtract from the current one |
|---|
| 573 | |
|---|
| 574 | :return: new data set |
|---|
| 575 | |
|---|
| 576 | :raise ValueError: raised when two data sets are incompatible |
|---|
| 577 | |
|---|
| 578 | """ |
|---|
| 579 | def operation(a, b): |
|---|
| 580 | return a * b |
|---|
| 581 | return self._perform_operation(other, operation) |
|---|
| 582 | |
|---|
| 583 | def __rmul__(self, other): |
|---|
| 584 | """ |
|---|
| 585 | Multiply two data sets |
|---|
| 586 | |
|---|
| 587 | :param other: data set to subtract from the current one |
|---|
| 588 | |
|---|
| 589 | :return: new data set |
|---|
| 590 | |
|---|
| 591 | :raise ValueError: raised when two data sets are incompatible |
|---|
| 592 | """ |
|---|
| 593 | def operation(a, b): |
|---|
| 594 | return b * a |
|---|
| 595 | return self._perform_operation(other, operation) |
|---|
| 596 | |
|---|
| 597 | def __div__(self, other): |
|---|
| 598 | """ |
|---|
| 599 | Divided a data set by another |
|---|
| 600 | |
|---|
| 601 | :param other: data set that the current one is divided by |
|---|
| 602 | |
|---|
| 603 | :return: new data set |
|---|
| 604 | |
|---|
| 605 | :raise ValueError: raised when two data sets are incompatible |
|---|
| 606 | |
|---|
| 607 | """ |
|---|
| 608 | def operation(a, b): |
|---|
| 609 | return a/b |
|---|
| 610 | return self._perform_operation(other, operation) |
|---|
| 611 | |
|---|
| 612 | def __rdiv__(self, other): |
|---|
| 613 | """ |
|---|
| 614 | Divided a data set by another |
|---|
| 615 | |
|---|
| 616 | :param other: data set that the current one is divided by |
|---|
| 617 | |
|---|
| 618 | :return: new data set |
|---|
| 619 | |
|---|
| 620 | :raise ValueError: raised when two data sets are incompatible |
|---|
| 621 | |
|---|
| 622 | """ |
|---|
| 623 | def operation(a, b): |
|---|
| 624 | return b/a |
|---|
| 625 | return self._perform_operation(other, operation) |
|---|
| 626 | |
|---|
| 627 | |
|---|
| 628 | class Data1D(plottable_1D, DataInfo): |
|---|
| 629 | """ |
|---|
| 630 | 1D data class |
|---|
| 631 | """ |
|---|
| 632 | x_unit = '1/A' |
|---|
| 633 | y_unit = '1/cm' |
|---|
| 634 | |
|---|
| 635 | def __init__(self, x, y, dx=None, dy=None): |
|---|
| 636 | DataInfo.__init__(self) |
|---|
| 637 | plottable_1D.__init__(self, x, y, dx, dy) |
|---|
| 638 | |
|---|
| 639 | def __str__(self): |
|---|
| 640 | """ |
|---|
| 641 | Nice printout |
|---|
| 642 | """ |
|---|
| 643 | _str = "%s\n" % DataInfo.__str__(self) |
|---|
| 644 | |
|---|
| 645 | _str += "Data:\n" |
|---|
| 646 | _str += " Type: %s\n" % self.__class__.__name__ |
|---|
| 647 | _str += " X-axis: %s\t[%s]\n" % (self._xaxis, self._xunit) |
|---|
| 648 | _str += " Y-axis: %s\t[%s]\n" % (self._yaxis, self._yunit) |
|---|
| 649 | _str += " Length: %g\n" % len(self.x) |
|---|
| 650 | |
|---|
| 651 | return _str |
|---|
| 652 | |
|---|
| 653 | def is_slit_smeared(self): |
|---|
| 654 | """ |
|---|
| 655 | Check whether the data has slit smearing information |
|---|
| 656 | |
|---|
| 657 | :return: True is slit smearing info is present, False otherwise |
|---|
| 658 | |
|---|
| 659 | """ |
|---|
| 660 | def _check(v): |
|---|
| 661 | if (v.__class__ == list or v.__class__ == numpy.ndarray) \ |
|---|
| 662 | and len(v) > 0 and min(v) > 0: |
|---|
| 663 | return True |
|---|
| 664 | |
|---|
| 665 | return False |
|---|
| 666 | |
|---|
| 667 | return _check(self.dxl) or _check(self.dxw) |
|---|
| 668 | |
|---|
| 669 | def clone_without_data(self, length=0, clone=None): |
|---|
| 670 | """ |
|---|
| 671 | Clone the current object, without copying the data (which |
|---|
| 672 | will be filled out by a subsequent operation). |
|---|
| 673 | The data arrays will be initialized to zero. |
|---|
| 674 | |
|---|
| 675 | :param length: length of the data array to be initialized |
|---|
| 676 | :param clone: if provided, the data will be copied to clone |
|---|
| 677 | """ |
|---|
| 678 | from copy import deepcopy |
|---|
| 679 | |
|---|
| 680 | if clone is None or not issubclass(clone.__class__, Data1D): |
|---|
| 681 | x = numpy.zeros(length) |
|---|
| 682 | dx = numpy.zeros(length) |
|---|
| 683 | y = numpy.zeros(length) |
|---|
| 684 | dy = numpy.zeros(length) |
|---|
| 685 | clone = Data1D(x, y, dx=dx, dy=dy) |
|---|
| 686 | |
|---|
| 687 | clone.title = self.title |
|---|
| 688 | clone.run = self.run |
|---|
| 689 | clone.filename = self.filename |
|---|
| 690 | clone.instrument = self.instrument |
|---|
| 691 | clone.notes = deepcopy(self.notes) |
|---|
| 692 | clone.process = deepcopy(self.process) |
|---|
| 693 | clone.detector = deepcopy(self.detector) |
|---|
| 694 | clone.sample = deepcopy(self.sample) |
|---|
| 695 | clone.source = deepcopy(self.source) |
|---|
| 696 | clone.collimation = deepcopy(self.collimation) |
|---|
| 697 | clone.meta_data = deepcopy(self.meta_data) |
|---|
| 698 | clone.errors = deepcopy(self.errors) |
|---|
| 699 | |
|---|
| 700 | return clone |
|---|
| 701 | |
|---|
| 702 | def _validity_check(self, other): |
|---|
| 703 | """ |
|---|
| 704 | Checks that the data lengths are compatible. |
|---|
| 705 | Checks that the x vectors are compatible. |
|---|
| 706 | Returns errors vectors equal to original |
|---|
| 707 | errors vectors if they were present or vectors |
|---|
| 708 | of zeros when none was found. |
|---|
| 709 | |
|---|
| 710 | :param other: other data set for operation |
|---|
| 711 | |
|---|
| 712 | :return: dy for self, dy for other [numpy arrays] |
|---|
| 713 | |
|---|
| 714 | :raise ValueError: when lengths are not compatible |
|---|
| 715 | |
|---|
| 716 | """ |
|---|
| 717 | dy_other = None |
|---|
| 718 | if isinstance(other, Data1D): |
|---|
| 719 | # Check that data lengths are the same |
|---|
| 720 | if len(self.x) != len(other.x) or \ |
|---|
| 721 | len(self.y) != len(other.y): |
|---|
| 722 | msg = "Unable to perform operation: data length are not equal" |
|---|
| 723 | raise ValueError, msg |
|---|
| 724 | |
|---|
| 725 | # Here we could also extrapolate between data points |
|---|
| 726 | for i in range(len(self.x)): |
|---|
| 727 | if self.x[i] != other.x[i]: |
|---|
| 728 | msg = "Incompatible data sets: x-values do not match" |
|---|
| 729 | raise ValueError, msg |
|---|
| 730 | |
|---|
| 731 | # Check that the other data set has errors, otherwise |
|---|
| 732 | # create zero vector |
|---|
| 733 | dy_other = other.dy |
|---|
| 734 | if other.dy == None or (len(other.dy) != len(other.y)): |
|---|
| 735 | dy_other = numpy.zeros(len(other.y)) |
|---|
| 736 | |
|---|
| 737 | # Check that we have errors, otherwise create zero vector |
|---|
| 738 | dy = self.dy |
|---|
| 739 | if self.dy == None or (len(self.dy) != len(self.y)): |
|---|
| 740 | dy = numpy.zeros(len(self.y)) |
|---|
| 741 | |
|---|
| 742 | return dy, dy_other |
|---|
| 743 | |
|---|
| 744 | def _perform_operation(self, other, operation): |
|---|
| 745 | """ |
|---|
| 746 | """ |
|---|
| 747 | # First, check the data compatibility |
|---|
| 748 | dy, dy_other = self._validity_check(other) |
|---|
| 749 | result = self.clone_without_data(len(self.x)) |
|---|
| 750 | |
|---|
| 751 | for i in range(len(self.x)): |
|---|
| 752 | result.x[i] = self.x[i] |
|---|
| 753 | if self.dx is not None and len(self.x) == len(self.dx): |
|---|
| 754 | result.dx[i] = self.dx[i] |
|---|
| 755 | |
|---|
| 756 | a = Uncertainty(self.y[i], dy[i]**2) |
|---|
| 757 | if isinstance(other, Data1D): |
|---|
| 758 | b = Uncertainty(other.y[i], dy_other[i]**2) |
|---|
| 759 | else: |
|---|
| 760 | b = other |
|---|
| 761 | |
|---|
| 762 | output = operation(a, b) |
|---|
| 763 | result.y[i] = output.x |
|---|
| 764 | result.dy[i] = math.sqrt(math.fabs(output.variance)) |
|---|
| 765 | return result |
|---|
| 766 | |
|---|
| 767 | |
|---|
| 768 | class Data2D(plottable_2D, DataInfo): |
|---|
| 769 | """ |
|---|
| 770 | 2D data class |
|---|
| 771 | """ |
|---|
| 772 | ## Units for Q-values |
|---|
| 773 | Q_unit = '1/A' |
|---|
| 774 | |
|---|
| 775 | ## Units for I(Q) values |
|---|
| 776 | I_unit = '1/cm' |
|---|
| 777 | |
|---|
| 778 | ## Vector of Q-values at the center of each bin in x |
|---|
| 779 | x_bins = None |
|---|
| 780 | |
|---|
| 781 | ## Vector of Q-values at the center of each bin in y |
|---|
| 782 | y_bins = None |
|---|
| 783 | |
|---|
| 784 | def __init__(self, data=None, err_data=None, qx_data=None, |
|---|
| 785 | qy_data=None, q_data=None, mask=None, |
|---|
| 786 | dqx_data=None, dqy_data=None): |
|---|
| 787 | self.y_bins = [] |
|---|
| 788 | self.x_bins = [] |
|---|
| 789 | DataInfo.__init__(self) |
|---|
| 790 | plottable_2D.__init__(self, data, err_data, qx_data, |
|---|
| 791 | qy_data, q_data, mask, dqx_data, dqy_data) |
|---|
| 792 | if len(self.detector) > 0: |
|---|
| 793 | raise RuntimeError, "Data2D: Detector bank already filled at init" |
|---|
| 794 | |
|---|
| 795 | def __str__(self): |
|---|
| 796 | _str = "%s\n" % DataInfo.__str__(self) |
|---|
| 797 | |
|---|
| 798 | _str += "Data:\n" |
|---|
| 799 | _str += " Type: %s\n" % self.__class__.__name__ |
|---|
| 800 | _str += " X- & Y-axis: %s\t[%s]\n" % (self._yaxis, self._yunit) |
|---|
| 801 | _str += " Z-axis: %s\t[%s]\n" % (self._zaxis, self._zunit) |
|---|
| 802 | #leny = 0 |
|---|
| 803 | #if len(self.data) > 0: |
|---|
| 804 | # leny = len(self.data) |
|---|
| 805 | _str += " Length: %g \n" % (len(self.data)) |
|---|
| 806 | |
|---|
| 807 | return _str |
|---|
| 808 | |
|---|
| 809 | def clone_without_data(self, length=0, clone=None): |
|---|
| 810 | """ |
|---|
| 811 | Clone the current object, without copying the data (which |
|---|
| 812 | will be filled out by a subsequent operation). |
|---|
| 813 | The data arrays will be initialized to zero. |
|---|
| 814 | |
|---|
| 815 | :param length: length of the data array to be initialized |
|---|
| 816 | :param clone: if provided, the data will be copied to clone |
|---|
| 817 | """ |
|---|
| 818 | from copy import deepcopy |
|---|
| 819 | |
|---|
| 820 | if clone is None or not issubclass(clone.__class__, Data2D): |
|---|
| 821 | data = numpy.zeros(length) |
|---|
| 822 | err_data = numpy.zeros(length) |
|---|
| 823 | qx_data = numpy.zeros(length) |
|---|
| 824 | qy_data = numpy.zeros(length) |
|---|
| 825 | q_data = numpy.zeros(length) |
|---|
| 826 | mask = numpy.zeros(length) |
|---|
| 827 | dqx_data = None |
|---|
| 828 | dqy_data = None |
|---|
| 829 | clone = Data2D(data, err_data, qx_data, qy_data, |
|---|
| 830 | q_data, mask, dqx_data=dqx_data, dqy_data=dqy_data) |
|---|
| 831 | |
|---|
| 832 | clone.title = self.title |
|---|
| 833 | clone.run = self.run |
|---|
| 834 | clone.filename = self.filename |
|---|
| 835 | clone.instrument = self.instrument |
|---|
| 836 | clone.notes = deepcopy(self.notes) |
|---|
| 837 | clone.process = deepcopy(self.process) |
|---|
| 838 | clone.detector = deepcopy(self.detector) |
|---|
| 839 | clone.sample = deepcopy(self.sample) |
|---|
| 840 | clone.source = deepcopy(self.source) |
|---|
| 841 | clone.collimation = deepcopy(self.collimation) |
|---|
| 842 | clone.meta_data = deepcopy(self.meta_data) |
|---|
| 843 | clone.errors = deepcopy(self.errors) |
|---|
| 844 | |
|---|
| 845 | return clone |
|---|
| 846 | |
|---|
| 847 | def _validity_check(self, other): |
|---|
| 848 | """ |
|---|
| 849 | Checks that the data lengths are compatible. |
|---|
| 850 | Checks that the x vectors are compatible. |
|---|
| 851 | Returns errors vectors equal to original |
|---|
| 852 | errors vectors if they were present or vectors |
|---|
| 853 | of zeros when none was found. |
|---|
| 854 | |
|---|
| 855 | :param other: other data set for operation |
|---|
| 856 | |
|---|
| 857 | :return: dy for self, dy for other [numpy arrays] |
|---|
| 858 | |
|---|
| 859 | :raise ValueError: when lengths are not compatible |
|---|
| 860 | |
|---|
| 861 | """ |
|---|
| 862 | err_other = None |
|---|
| 863 | if isinstance(other, Data2D): |
|---|
| 864 | # Check that data lengths are the same |
|---|
| 865 | if numpy.size(self.data) != numpy.size(other.data): |
|---|
| 866 | msg = "Unable to perform operation: data length are not equal" |
|---|
| 867 | raise ValueError, msg |
|---|
| 868 | |
|---|
| 869 | # Check that the scales match |
|---|
| 870 | #TODO: matching scales? |
|---|
| 871 | |
|---|
| 872 | # Check that the other data set has errors, otherwise |
|---|
| 873 | # create zero vector |
|---|
| 874 | #TODO: test this |
|---|
| 875 | err_other = other.err_data |
|---|
| 876 | if other.err_data == None or \ |
|---|
| 877 | (numpy.size(other.err_data) != numpy.size(other.data)): |
|---|
| 878 | err_other = numpy.zeros([numpy.size(other.data, 0), |
|---|
| 879 | numpy.size(other.data, 1)]) |
|---|
| 880 | |
|---|
| 881 | # Check that we have errors, otherwise create zero vector |
|---|
| 882 | err = self.err_data |
|---|
| 883 | if self.err_data == None or \ |
|---|
| 884 | (numpy.size(self.err_data) != numpy.size(self.data)): |
|---|
| 885 | err = numpy.zeros([numpy.size(self.data, 0), |
|---|
| 886 | numpy.size(self.data, 1)]) |
|---|
| 887 | |
|---|
| 888 | return err, err_other |
|---|
| 889 | |
|---|
| 890 | def _perform_operation(self, other, operation): |
|---|
| 891 | """ |
|---|
| 892 | Perform 2D operations between data sets |
|---|
| 893 | |
|---|
| 894 | :param other: other data set |
|---|
| 895 | :param operation: function defining the operation |
|---|
| 896 | |
|---|
| 897 | """ |
|---|
| 898 | # First, check the data compatibility |
|---|
| 899 | dy, dy_other = self._validity_check(other) |
|---|
| 900 | |
|---|
| 901 | result = self.clone_without_data([numpy.size(self.data, 0), |
|---|
| 902 | numpy.size(self.data, 1)]) |
|---|
| 903 | |
|---|
| 904 | for i in range(numpy.size(self.data, 0)): |
|---|
| 905 | for j in range(numpy.size(self.data, 1)): |
|---|
| 906 | result.data[i][j] = self.data[i][j] |
|---|
| 907 | if self.err_data is not None and \ |
|---|
| 908 | numpy.size(self.data) == numpy.size(self.err_data): |
|---|
| 909 | result.err_data[i][j] = self.err_data[i][j] |
|---|
| 910 | |
|---|
| 911 | a = Uncertainty(self.data[i][j], dy[i][j]**2) |
|---|
| 912 | if isinstance(other, Data2D): |
|---|
| 913 | b = Uncertainty(other.data[i][j], dy_other[i][j]**2) |
|---|
| 914 | else: |
|---|
| 915 | b = other |
|---|
| 916 | |
|---|
| 917 | output = operation(a, b) |
|---|
| 918 | result.data[i][j] = output.x |
|---|
| 919 | result.err_data[i][j] = math.sqrt(math.fabs(output.variance)) |
|---|
| 920 | return result |
|---|
