1 | """This module contains various auxiliary function used by pyvolution. |
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2 | |
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3 | It is also a clearing house for functions that may later earn a module |
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4 | of their own. |
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5 | """ |
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6 | |
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7 | |
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8 | #FIXME: Deprecate this shortcut |
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9 | from utilities.numerical_tools import ensure_numeric |
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10 | |
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11 | import utilities.polygon |
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12 | from warnings import warn |
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13 | |
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14 | def point_on_line(*args, **kwargs): |
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15 | """Temporary Interface to new location""" |
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16 | |
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17 | msg = 'point_on_line has moved from util.py. ' |
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18 | msg += 'Please use "from utilities.polygon import point_on_line"' |
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19 | warn(msg, DeprecationWarning) |
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20 | |
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21 | return utilities.polygon.point_on_line(*args, **kwargs) |
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22 | |
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23 | def inside_polygon(*args, **kwargs): |
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24 | """Temporary Interface to new location""" |
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25 | |
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26 | print 'inside_polygon has moved from util.py. ', |
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27 | print 'Please use "from utilities.polygon import inside_polygon"' |
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28 | |
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29 | return utilities.polygon.inside_polygon(*args, **kwargs) |
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30 | |
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31 | def outside_polygon(*args, **kwargs): |
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32 | """Temporary Interface to new location""" |
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33 | |
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34 | print 'outside_polygon has moved from util.py. ', |
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35 | print 'Please use "from utilities.polygon import outside_polygon"' |
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36 | |
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37 | return utilities.polygon.outside_polygon(*args, **kwargs) |
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38 | |
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39 | |
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40 | def separate_points_by_polygon(*args, **kwargs): |
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41 | """Temporary Interface to new location""" |
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42 | |
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43 | print 'separate_points_by_polygon has moved from util.py. ', |
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44 | print 'Please use "from utilities.polygon import separate_points_by_polygon"' |
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45 | |
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46 | return utilities.polygon.separate_points_by_polygon(*args, **kwargs) |
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47 | |
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48 | |
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49 | from utilities.polygon import Polygon_function #No warning |
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50 | |
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51 | |
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52 | def read_polygon(*args, **kwargs): |
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53 | """Temporary Interface to new location""" |
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54 | |
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55 | print 'read_polygon has moved from util.py. ', |
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56 | print 'Please use "from utilities.polygon import read_polygon"' |
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57 | |
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58 | return utilities.polygon.read_polygon(*args, **kwargs) |
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59 | |
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60 | |
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61 | def populate_polygon(*args, **kwargs): |
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62 | """Temporary Interface to new location""" |
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63 | |
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64 | print 'populate_polygon has moved from util.py. ', |
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65 | print 'Please use "from utilities.polygon import populate_polygon"' |
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66 | |
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67 | return utilities.polygon.populate_polygon(*args, **kwargs) |
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68 | |
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69 | def read_xya(filename): |
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70 | """Read simple xya file, possibly with a header in the first line, just |
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71 | x y [attributes] |
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72 | separated by whitespace |
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73 | |
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74 | Format can be either ASCII or NetCDF |
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75 | |
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76 | Return list of points, list of attributes and |
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77 | attribute names if present otherwise None |
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78 | """ |
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79 | print "read_xya is obsolete. Use import_points_file from load_mesh.loadASCII" |
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80 | #FIXME: Probably obsoleted by similar function in load_ASCII |
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81 | #FIXME: Name read_data_points (or see 'load' in pylab) |
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82 | |
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83 | |
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84 | from load_mesh.loadASCII import import_points_file |
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85 | |
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86 | points_dict = import_points_file(filename) |
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87 | return points_dict['pointlist'], points_dict['attributelist'] |
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88 | |
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89 | |
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90 | |
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91 | |
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92 | #Normal util stuff |
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93 | |
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94 | def angle(v): |
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95 | """Compute angle between e1 (the unit vector in the x-direction) |
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96 | and the specified vector |
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97 | """ |
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98 | |
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99 | from math import acos, pi, sqrt |
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100 | from Numeric import sum, array |
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101 | |
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102 | l = sqrt( sum (array(v)**2)) |
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103 | v1 = v[0]/l |
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104 | v2 = v[1]/l |
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105 | |
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106 | |
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107 | theta = acos(v1) |
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108 | |
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109 | #try: |
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110 | # theta = acos(v1) |
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111 | #except ValueError, e: |
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112 | # print 'WARNING (util.py): Angle acos(%s) failed: %s' %(str(v1), e) |
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113 | # |
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114 | # #FIXME, hack to avoid acos(1.0) Value error |
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115 | # # why is it happening? |
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116 | # # is it catching something we should avoid? |
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117 | # #FIXME (Ole): When did this happen? We need a unit test to |
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118 | # #reveal this condition or otherwise remove the hack |
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119 | # |
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120 | # s = 1e-6 |
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121 | # if (v1+s > 1.0) and (v1-s < 1.0) : |
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122 | # theta = 0.0 |
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123 | # elif (v1+s > -1.0) and (v1-s < -1.0): |
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124 | # theta = 3.1415926535897931 |
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125 | # print 'WARNING (util.py): angle v1 is %f, setting acos to %f '\ |
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126 | # %(v1, theta) |
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127 | |
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128 | if v2 < 0: |
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129 | #Quadrant 3 or 4 |
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130 | theta = 2*pi-theta |
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131 | |
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132 | return theta |
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133 | |
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134 | |
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135 | def anglediff(v0, v1): |
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136 | """Compute difference between angle of vector x0, y0 and x1, y1. |
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137 | This is used for determining the ordering of vertices, |
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138 | e.g. for checking if they are counter clockwise. |
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139 | |
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140 | Always return a positive value |
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141 | """ |
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142 | |
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143 | from math import pi |
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144 | |
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145 | a0 = angle(v0) |
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146 | a1 = angle(v1) |
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147 | |
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148 | #Ensure that difference will be positive |
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149 | if a0 < a1: |
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150 | a0 += 2*pi |
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151 | |
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152 | return a0-a1 |
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153 | |
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154 | |
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155 | def mean(x): |
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156 | from Numeric import sum |
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157 | return sum(x)/len(x) |
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158 | |
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159 | |
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160 | |
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161 | |
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162 | def file_function(filename, |
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163 | domain = None, |
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164 | quantities = None, |
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165 | interpolation_points = None, |
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166 | verbose = False, |
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167 | use_cache = False): |
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168 | """Read time history of spatial data from NetCDF file and return |
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169 | a callable object. |
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170 | |
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171 | Input variables: |
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172 | |
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173 | filename - Name of sww or tms file |
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174 | |
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175 | If the file has extension 'sww' then it is assumed to be spatio-temporal |
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176 | or temporal and the callable object will have the form f(t,x,y) or f(t) |
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177 | depending on whether the file contains spatial data |
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178 | |
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179 | If the file has extension 'tms' then it is assumed to be temporal only |
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180 | and the callable object will have the form f(t) |
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181 | |
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182 | Either form will return interpolated values based on the input file |
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183 | using the underlying interpolation_function. |
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184 | |
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185 | domain - Associated domain object |
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186 | If domain is specified, model time (domain.starttime) |
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187 | will be checked and possibly modified. |
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188 | |
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189 | All times are assumed to be in UTC |
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190 | |
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191 | All spatial information is assumed to be in absolute UTM coordinates. |
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192 | |
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193 | quantities - the name of the quantity to be interpolated or a |
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194 | list of quantity names. The resulting function will return |
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195 | a tuple of values - one for each quantity |
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196 | |
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197 | interpolation_points - list of absolute UTM coordinates for points at |
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198 | which values are sought |
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199 | |
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200 | use_cache: True means that caching of intermediate result of |
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201 | Interpolation_function is attempted |
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202 | |
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203 | |
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204 | See Interpolation function for further documentation |
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205 | """ |
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206 | |
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207 | |
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208 | if use_cache is True: |
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209 | try: |
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210 | from caching import cache |
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211 | except: |
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212 | msg = 'Caching was requested, but caching module'+\ |
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213 | 'could not be imported' |
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214 | raise msg |
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215 | |
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216 | |
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217 | f = cache(_file_function, |
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218 | filename, |
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219 | {'domain': domain, |
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220 | 'quantities': quantities, |
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221 | 'interpolation_points': interpolation_points, |
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222 | 'verbose': verbose}, |
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223 | dependencies = [filename], |
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224 | compression = False, |
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225 | verbose = verbose) |
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226 | #FIXME (Ole): Pass cache arguments, such as compression, in some sort of |
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227 | #structure |
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228 | |
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229 | else: |
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230 | f = _file_function(filename, |
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231 | domain, |
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232 | quantities, |
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233 | interpolation_points, |
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234 | verbose) |
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235 | |
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236 | return f |
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237 | |
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238 | |
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239 | |
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240 | def _file_function(filename, |
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241 | domain = None, |
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242 | quantities = None, |
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243 | interpolation_points = None, |
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244 | verbose = False): |
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245 | """Internal function |
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246 | |
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247 | See file_function for documentatiton |
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248 | """ |
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249 | |
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250 | |
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251 | #FIXME (OLE): Should check origin of domain against that of file |
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252 | #In fact, this is where origin should be converted to that of domain |
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253 | #Also, check that file covers domain fully. |
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254 | #If we use the suggested Point_set class for interpolation points |
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255 | #here it would be easier |
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256 | |
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257 | #Take into account: |
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258 | #- domain's georef |
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259 | #- sww file's georef |
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260 | #- interpolation points as absolute UTM coordinates |
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261 | |
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262 | |
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263 | assert type(filename) == type(''),\ |
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264 | 'First argument to File_function must be a string' |
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265 | |
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266 | try: |
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267 | fid = open(filename) |
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268 | except Exception, e: |
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269 | msg = 'File "%s" could not be opened: Error="%s"'\ |
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270 | %(filename, e) |
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271 | raise msg |
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272 | |
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273 | line = fid.readline() |
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274 | fid.close() |
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275 | |
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276 | if quantities is None: |
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277 | if domain is not None: |
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278 | quantities = domain.conserved_quantities |
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279 | |
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280 | |
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281 | |
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282 | if line[:3] == 'CDF': |
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283 | return get_netcdf_file_function(filename, domain, quantities, |
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284 | interpolation_points, |
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285 | verbose = verbose) |
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286 | else: |
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287 | raise 'Must be a NetCDF File' |
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288 | |
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289 | |
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290 | |
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291 | def get_netcdf_file_function(filename, |
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292 | domain=None, |
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293 | quantity_names=None, |
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294 | interpolation_points=None, |
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295 | verbose = False): |
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296 | """Read time history of spatial data from NetCDF sww file and |
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297 | return a callable object f(t,x,y) |
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298 | which will return interpolated values based on the input file. |
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299 | |
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300 | If domain is specified, model time (domain.starttime) |
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301 | will be checked and possibly modified |
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302 | |
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303 | All times are assumed to be in UTC |
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304 | |
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305 | See Interpolation function for further documetation |
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306 | |
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307 | """ |
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308 | |
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309 | |
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310 | #FIXME: Check that model origin is the same as file's origin |
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311 | #(both in UTM coordinates) |
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312 | #If not - modify those from file to match domain |
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313 | #Take this code from e.g. dem2pts in data_manager.py |
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314 | #FIXME: Use geo_reference to read and write xllcorner... |
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315 | |
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316 | |
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317 | #FIXME: Maybe move caching out to this level rather than at the |
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318 | #Interpolation_function level (below) |
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319 | |
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320 | import time, calendar, types |
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321 | from config import time_format |
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322 | from Scientific.IO.NetCDF import NetCDFFile |
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323 | from Numeric import array, zeros, Float, alltrue, concatenate, reshape |
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324 | from util import ensure_numeric |
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325 | |
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326 | #Open NetCDF file |
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327 | if verbose: print 'Reading', filename |
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328 | fid = NetCDFFile(filename, 'r') |
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329 | |
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330 | if type(quantity_names) == types.StringType: |
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331 | quantity_names = [quantity_names] |
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332 | |
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333 | if quantity_names is None or len(quantity_names) < 1: |
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334 | #If no quantities are specified get quantities from file |
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335 | #x, y, time are assumed as the independent variables so |
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336 | #they are excluded as potentiol quantities |
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337 | quantity_names = [] |
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338 | for name in fid.variables.keys(): |
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339 | if name not in ['x', 'y', 'time']: |
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340 | quantity_names.append(name) |
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341 | |
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342 | if len(quantity_names) < 1: |
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343 | msg = 'ERROR: At least one independent value must be specified' |
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344 | raise msg |
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345 | |
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346 | |
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347 | if interpolation_points is not None: |
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348 | interpolation_points = ensure_numeric(interpolation_points, Float) |
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349 | |
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350 | |
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351 | |
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352 | #Now assert that requested quantitites (and the independent ones) |
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353 | #are present in file |
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354 | missing = [] |
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355 | for quantity in ['time'] + quantity_names: |
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356 | if not fid.variables.has_key(quantity): |
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357 | missing.append(quantity) |
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358 | |
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359 | if len(missing) > 0: |
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360 | msg = 'Quantities %s could not be found in file %s'\ |
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361 | %(str(missing), filename) |
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362 | fid.close() |
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363 | raise msg |
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364 | |
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365 | #Decide whether this data has a spatial dimension |
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366 | spatial = True |
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367 | for quantity in ['x', 'y']: |
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368 | if not fid.variables.has_key(quantity): |
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369 | spatial = False |
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370 | |
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371 | if filename[-3:] == 'tms' and spatial is True: |
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372 | msg = 'Files of type tms must not contain spatial information' |
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373 | raise msg |
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374 | |
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375 | if filename[-3:] == 'sww' and spatial is False: |
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376 | msg = 'Files of type sww must contain spatial information' |
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377 | raise msg |
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378 | |
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379 | #Get first timestep |
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380 | try: |
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381 | starttime = fid.starttime[0] |
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382 | except ValueError: |
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383 | msg = 'Could not read starttime from file %s' %filename |
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384 | raise msg |
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385 | |
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386 | #Get variables |
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387 | if verbose: print 'Get variables' |
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388 | time = fid.variables['time'][:] |
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389 | |
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390 | if spatial: |
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391 | #Get origin |
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392 | xllcorner = fid.xllcorner[0] |
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393 | yllcorner = fid.yllcorner[0] |
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394 | zone = fid.zone[0] |
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395 | |
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396 | x = fid.variables['x'][:] |
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397 | y = fid.variables['y'][:] |
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398 | triangles = fid.variables['volumes'][:] |
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399 | |
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400 | x = reshape(x, (len(x),1)) |
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401 | y = reshape(y, (len(y),1)) |
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402 | vertex_coordinates = concatenate((x,y), axis=1) #m x 2 array |
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403 | |
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404 | if interpolation_points is not None: |
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405 | #Adjust for georef |
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406 | interpolation_points[:,0] -= xllcorner |
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407 | interpolation_points[:,1] -= yllcorner |
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408 | |
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409 | |
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410 | |
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411 | |
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412 | if domain is not None: |
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413 | #Update domain.startime if it is *earlier* than starttime |
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414 | if starttime > domain.starttime: |
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415 | msg = 'WARNING: Start time as specified in domain (%f)'\ |
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416 | %domain.starttime |
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417 | msg += ' is earlier than the starttime of file %s (%f).'\ |
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418 | %(filename, starttime) |
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419 | msg += ' Modifying domain starttime accordingly.' |
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420 | |
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421 | if verbose: print msg |
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422 | domain.starttime = starttime #Modifying model time |
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423 | if verbose: print 'Domain starttime is now set to %f'\ |
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424 | %domain.starttime |
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425 | |
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426 | |
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427 | #If domain.startime is *later* than starttime, |
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428 | #move time back - relative to domain's time |
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429 | if domain.starttime > starttime: |
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430 | time = time - domain.starttime + starttime |
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431 | |
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432 | #FIXME Use method in geo to reconcile |
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433 | #if spatial: |
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434 | #assert domain.geo_reference.xllcorner == xllcorner |
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435 | #assert domain.geo_reference.yllcorner == yllcorner |
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436 | #assert domain.geo_reference.zone == zone |
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437 | |
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438 | if verbose: |
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439 | print 'File_function data obtained from: %s' %filename |
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440 | print ' References:' |
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441 | #print ' Datum ....' #FIXME |
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442 | if spatial: |
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443 | print ' Lower left corner: [%f, %f]'\ |
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444 | %(xllcorner, yllcorner) |
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445 | print ' Start time: %f' %starttime |
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446 | |
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447 | |
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448 | #Produce values for desired data points at |
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449 | #each timestep |
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450 | |
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451 | quantities = {} |
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452 | for i, name in enumerate(quantity_names): |
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453 | quantities[name] = fid.variables[name][:] |
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454 | fid.close() |
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455 | |
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456 | |
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457 | from least_squares import Interpolation_function |
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458 | |
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459 | if not spatial: |
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460 | vertex_coordinates = triangles = interpolation_points = None |
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461 | |
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462 | |
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463 | return Interpolation_function(time, |
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464 | quantities, |
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465 | quantity_names, |
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466 | vertex_coordinates, |
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467 | triangles, |
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468 | interpolation_points, |
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469 | verbose = verbose) |
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470 | |
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471 | |
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472 | |
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473 | |
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474 | def tsh2sww(filename, verbose=True): |
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475 | """ |
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476 | to check if a tsh/msh file 'looks' good. |
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477 | """ |
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478 | |
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479 | #FIXME Move to data_manager |
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480 | from shallow_water import Domain |
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481 | from pmesh2domain import pmesh_to_domain_instance |
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482 | import time, os |
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483 | from data_manager import get_dataobject |
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484 | from os import sep, path |
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485 | #from util import mean |
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486 | |
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487 | if verbose == True:print 'Creating domain from', filename |
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488 | domain = pmesh_to_domain_instance(filename, Domain) |
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489 | if verbose == True:print "Number of triangles = ", len(domain) |
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490 | |
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491 | domain.smooth = True |
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492 | domain.format = 'sww' #Native netcdf visualisation format |
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493 | file_path, filename = path.split(filename) |
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494 | filename, ext = path.splitext(filename) |
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495 | domain.filename = filename |
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496 | domain.reduction = mean |
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497 | if verbose == True:print "file_path",file_path |
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498 | if file_path == "":file_path = "." |
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499 | domain.set_datadir(file_path) |
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500 | |
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501 | if verbose == True: |
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502 | print "Output written to " + domain.get_datadir() + sep + \ |
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503 | domain.filename + "." + domain.format |
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504 | sww = get_dataobject(domain) |
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505 | sww.store_connectivity() |
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506 | sww.store_timestep('stage') |
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507 | |
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508 | |
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509 | |
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510 | |
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511 | def multiple_replace(text, dictionary): |
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512 | """Multiple replace of words in text |
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513 | |
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514 | text: String to be modified |
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515 | dictionary: Mapping of words that are to be substituted |
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516 | |
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517 | Python Cookbook 3.14 page 88 and page 90 |
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518 | """ |
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519 | |
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520 | import re |
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521 | |
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522 | #Create a regular expression from all of the dictionary keys |
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523 | #matching only entire words |
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524 | regex = re.compile(r'\b'+ \ |
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525 | r'\b|\b'.join(map(re.escape, dictionary.keys()))+ \ |
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526 | r'\b' ) |
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527 | |
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528 | #For each match, lookup the corresponding value in the dictionary |
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529 | return regex.sub(lambda match: dictionary[match.group(0)], text) |
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530 | |
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531 | |
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532 | |
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533 | |
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534 | def apply_expression_to_dictionary(expression, dictionary):#dictionary): |
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535 | """Apply arbitrary expression to values of dictionary |
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536 | |
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537 | Given an expression in terms of the keys, replace key by the |
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538 | corresponding values and evaluate. |
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539 | |
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540 | |
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541 | expression: Arbitrary, e.g. arithmetric, expression relating keys |
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542 | from dictionary. |
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543 | |
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544 | dictionary: Mapping between symbols in expression and objects that |
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545 | will be evaluated by expression. |
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546 | Values in dictionary must support operators given in |
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547 | expression e.g. by overloading |
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548 | """ |
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549 | |
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550 | import types |
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551 | import re |
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552 | |
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553 | assert isinstance(expression, basestring) |
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554 | assert type(dictionary) == types.DictType |
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555 | |
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556 | #Convert dictionary values to textual representations suitable for eval |
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557 | D = {} |
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558 | for key in dictionary: |
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559 | D[key] = 'dictionary["%s"]' %key |
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560 | |
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561 | #Perform substitution of variables |
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562 | expression = multiple_replace(expression, D) |
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563 | |
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564 | #Evaluate and return |
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565 | try: |
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566 | return eval(expression) |
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567 | except NameError, e: |
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568 | msg = 'Expression "%s" could not be evaluated: %s' %(expression, e) |
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569 | raise NameError, msg |
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570 | |
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571 | |
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572 | |
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573 | |
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574 | |
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575 | |
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576 | |
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577 | |
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578 | #################################################################### |
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579 | #Python versions of function that are also implemented in util_gateway.c |
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580 | # |
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581 | |
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582 | def gradient_python(x0, y0, x1, y1, x2, y2, q0, q1, q2): |
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583 | """ |
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584 | """ |
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585 | |
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586 | det = (y2-y0)*(x1-x0) - (y1-y0)*(x2-x0) |
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587 | a = (y2-y0)*(q1-q0) - (y1-y0)*(q2-q0) |
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588 | a /= det |
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589 | |
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590 | b = (x1-x0)*(q2-q0) - (x2-x0)*(q1-q0) |
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591 | b /= det |
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592 | |
---|
593 | return a, b |
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594 | |
---|
595 | |
---|
596 | def gradient2_python(x0, y0, x1, y1, q0, q1): |
---|
597 | """Compute radient based on two points and enforce zero gradient |
---|
598 | in the direction orthogonal to (x1-x0), (y1-y0) |
---|
599 | """ |
---|
600 | |
---|
601 | #Old code |
---|
602 | #det = x0*y1 - x1*y0 |
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603 | #if det != 0.0: |
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604 | # a = (y1*q0 - y0*q1)/det |
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605 | # b = (x0*q1 - x1*q0)/det |
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606 | |
---|
607 | #Correct code (ON) |
---|
608 | det = (x1-x0)**2 + (y1-y0)**2 |
---|
609 | if det != 0.0: |
---|
610 | a = (x1-x0)*(q1-q0)/det |
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611 | b = (y1-y0)*(q1-q0)/det |
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612 | |
---|
613 | return a, b |
---|
614 | |
---|
615 | |
---|
616 | ############################################## |
---|
617 | #Initialise module |
---|
618 | |
---|
619 | from utilities import compile |
---|
620 | if compile.can_use_C_extension('util_ext.c'): |
---|
621 | from util_ext import gradient, gradient2#, point_on_line |
---|
622 | #separate_points_by_polygon = separate_points_by_polygon_c |
---|
623 | else: |
---|
624 | gradient = gradient_python |
---|
625 | gradient2 = gradient2_python |
---|
626 | |
---|
627 | |
---|
628 | if __name__ == "__main__": |
---|
629 | pass |
---|
630 | |
---|
631 | |
---|
632 | |
---|
633 | |
---|