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 | import anuga.utilities.polygon |
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9 | from warnings import warn |
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10 | |
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11 | |
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12 | |
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13 | def file_function(filename, |
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14 | domain = None, |
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15 | quantities = None, |
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16 | interpolation_points = None, |
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17 | verbose = False, |
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18 | use_cache = False): |
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19 | """Read time history of spatial data from NetCDF file and return |
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20 | a callable object. |
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21 | |
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22 | Input variables: |
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23 | |
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24 | filename - Name of sww or tms file |
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25 | |
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26 | If the file has extension 'sww' then it is assumed to be spatio-temporal |
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27 | or temporal and the callable object will have the form f(t,x,y) or f(t) |
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28 | depending on whether the file contains spatial data |
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29 | |
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30 | If the file has extension 'tms' then it is assumed to be temporal only |
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31 | and the callable object will have the form f(t) |
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32 | |
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33 | Either form will return interpolated values based on the input file |
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34 | using the underlying interpolation_function. |
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35 | |
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36 | domain - Associated domain object |
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37 | If domain is specified, model time (domain.starttime) |
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38 | will be checked and possibly modified. |
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39 | |
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40 | All times are assumed to be in UTC |
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41 | |
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42 | All spatial information is assumed to be in absolute UTM coordinates. |
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43 | |
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44 | quantities - the name of the quantity to be interpolated or a |
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45 | list of quantity names. The resulting function will return |
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46 | a tuple of values - one for each quantity |
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47 | |
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48 | interpolation_points - list of absolute UTM coordinates for points at |
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49 | which values are sought |
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50 | |
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51 | use_cache: True means that caching of intermediate result of |
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52 | Interpolation_function is attempted |
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53 | |
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54 | |
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55 | See Interpolation function for further documentation |
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56 | """ |
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57 | |
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58 | |
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59 | if use_cache is True: |
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60 | try: |
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61 | from caching import cache |
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62 | except: |
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63 | msg = 'Caching was requested, but caching module'+\ |
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64 | 'could not be imported' |
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65 | raise msg |
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66 | |
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67 | |
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68 | f = cache(_file_function, |
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69 | filename, |
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70 | {'domain': domain, |
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71 | 'quantities': quantities, |
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72 | 'interpolation_points': interpolation_points, |
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73 | 'verbose': verbose}, |
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74 | dependencies = [filename], |
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75 | compression = False, |
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76 | verbose = verbose) |
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77 | #FIXME (Ole): Pass cache arguments, such as compression, in some sort of |
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78 | #structure |
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79 | |
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80 | else: |
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81 | f = _file_function(filename, |
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82 | domain, |
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83 | quantities, |
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84 | interpolation_points, |
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85 | verbose) |
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86 | |
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87 | return f |
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88 | |
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89 | |
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90 | |
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91 | def _file_function(filename, |
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92 | domain = None, |
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93 | quantities = None, |
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94 | interpolation_points = None, |
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95 | verbose = False): |
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96 | """Internal function |
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97 | |
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98 | See file_function for documentatiton |
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99 | """ |
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100 | |
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101 | |
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102 | #FIXME (OLE): Should check origin of domain against that of file |
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103 | #In fact, this is where origin should be converted to that of domain |
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104 | #Also, check that file covers domain fully. |
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105 | #If we use the suggested Point_set class for interpolation points |
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106 | #here it would be easier |
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107 | |
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108 | #Take into account: |
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109 | #- domain's georef |
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110 | #- sww file's georef |
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111 | #- interpolation points as absolute UTM coordinates |
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112 | |
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113 | |
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114 | assert type(filename) == type(''),\ |
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115 | 'First argument to File_function must be a string' |
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116 | |
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117 | try: |
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118 | fid = open(filename) |
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119 | except Exception, e: |
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120 | msg = 'File "%s" could not be opened: Error="%s"'\ |
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121 | %(filename, e) |
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122 | raise msg |
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123 | |
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124 | line = fid.readline() |
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125 | fid.close() |
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126 | |
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127 | if quantities is None: |
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128 | if domain is not None: |
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129 | quantities = domain.conserved_quantities |
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130 | |
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131 | |
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132 | |
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133 | if line[:3] == 'CDF': |
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134 | return get_netcdf_file_function(filename, domain, quantities, |
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135 | interpolation_points, |
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136 | verbose = verbose) |
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137 | else: |
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138 | raise 'Must be a NetCDF File' |
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139 | |
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140 | |
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141 | |
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142 | def get_netcdf_file_function(filename, |
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143 | domain=None, |
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144 | quantity_names=None, |
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145 | interpolation_points=None, |
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146 | verbose = False): |
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147 | """Read time history of spatial data from NetCDF sww file and |
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148 | return a callable object f(t,x,y) |
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149 | which will return interpolated values based on the input file. |
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150 | |
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151 | If domain is specified, model time (domain.starttime) |
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152 | will be checked and possibly modified |
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153 | |
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154 | All times are assumed to be in UTC |
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155 | |
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156 | See Interpolation function for further documetation |
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157 | |
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158 | """ |
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159 | |
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160 | |
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161 | #FIXME: Check that model origin is the same as file's origin |
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162 | #(both in UTM coordinates) |
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163 | #If not - modify those from file to match domain |
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164 | #Take this code from e.g. dem2pts in data_manager.py |
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165 | #FIXME: Use geo_reference to read and write xllcorner... |
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166 | |
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167 | |
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168 | #FIXME: Maybe move caching out to this level rather than at the |
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169 | #Interpolation_function level (below) |
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170 | |
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171 | import time, calendar, types |
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172 | from config import time_format |
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173 | from Scientific.IO.NetCDF import NetCDFFile |
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174 | from Numeric import array, zeros, Float, alltrue, concatenate, reshape |
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175 | from anuga.utilities.numerical_tools import ensure_numeric |
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176 | |
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177 | #Open NetCDF file |
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178 | if verbose: print 'Reading', filename |
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179 | fid = NetCDFFile(filename, 'r') |
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180 | |
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181 | if type(quantity_names) == types.StringType: |
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182 | quantity_names = [quantity_names] |
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183 | |
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184 | if quantity_names is None or len(quantity_names) < 1: |
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185 | #If no quantities are specified get quantities from file |
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186 | #x, y, time are assumed as the independent variables so |
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187 | #they are excluded as potentiol quantities |
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188 | quantity_names = [] |
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189 | for name in fid.variables.keys(): |
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190 | if name not in ['x', 'y', 'time']: |
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191 | quantity_names.append(name) |
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192 | |
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193 | if len(quantity_names) < 1: |
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194 | msg = 'ERROR: At least one independent value must be specified' |
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195 | raise msg |
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196 | |
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197 | |
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198 | if interpolation_points is not None: |
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199 | interpolation_points = ensure_numeric(interpolation_points, Float) |
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200 | |
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201 | |
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202 | |
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203 | #Now assert that requested quantitites (and the independent ones) |
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204 | #are present in file |
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205 | missing = [] |
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206 | for quantity in ['time'] + quantity_names: |
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207 | if not fid.variables.has_key(quantity): |
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208 | missing.append(quantity) |
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209 | |
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210 | if len(missing) > 0: |
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211 | msg = 'Quantities %s could not be found in file %s'\ |
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212 | %(str(missing), filename) |
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213 | fid.close() |
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214 | raise msg |
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215 | |
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216 | #Decide whether this data has a spatial dimension |
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217 | spatial = True |
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218 | for quantity in ['x', 'y']: |
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219 | if not fid.variables.has_key(quantity): |
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220 | spatial = False |
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221 | |
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222 | if filename[-3:] == 'tms' and spatial is True: |
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223 | msg = 'Files of type tms must not contain spatial information' |
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224 | raise msg |
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225 | |
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226 | if filename[-3:] == 'sww' and spatial is False: |
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227 | msg = 'Files of type sww must contain spatial information' |
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228 | raise msg |
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229 | |
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230 | #Get first timestep |
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231 | try: |
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232 | starttime = fid.starttime[0] |
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233 | except ValueError: |
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234 | msg = 'Could not read starttime from file %s' %filename |
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235 | raise msg |
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236 | |
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237 | #Get variables |
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238 | if verbose: print 'Get variables' |
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239 | time = fid.variables['time'][:] |
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240 | |
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241 | if spatial: |
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242 | #Get origin |
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243 | xllcorner = fid.xllcorner[0] |
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244 | yllcorner = fid.yllcorner[0] |
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245 | zone = fid.zone[0] |
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246 | |
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247 | x = fid.variables['x'][:] |
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248 | y = fid.variables['y'][:] |
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249 | triangles = fid.variables['volumes'][:] |
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250 | |
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251 | x = reshape(x, (len(x),1)) |
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252 | y = reshape(y, (len(y),1)) |
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253 | vertex_coordinates = concatenate((x,y), axis=1) #m x 2 array |
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254 | |
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255 | if interpolation_points is not None: |
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256 | #Adjust for georef |
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257 | interpolation_points[:,0] -= xllcorner |
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258 | interpolation_points[:,1] -= yllcorner |
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259 | |
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260 | |
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261 | |
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262 | |
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263 | if domain is not None: |
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264 | #Update domain.startime if it is *earlier* than starttime |
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265 | if starttime > domain.starttime: |
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266 | msg = 'WARNING: Start time as specified in domain (%f)'\ |
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267 | %domain.starttime |
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268 | msg += ' is earlier than the starttime of file %s (%f).'\ |
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269 | %(filename, starttime) |
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270 | msg += ' Modifying domain starttime accordingly.' |
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271 | |
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272 | if verbose: print msg |
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273 | domain.starttime = starttime #Modifying model time |
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274 | if verbose: print 'Domain starttime is now set to %f'\ |
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275 | %domain.starttime |
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276 | |
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277 | |
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278 | #If domain.startime is *later* than starttime, |
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279 | #move time back - relative to domain's time |
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280 | if domain.starttime > starttime: |
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281 | time = time - domain.starttime + starttime |
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282 | |
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283 | #FIXME Use method in geo to reconcile |
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284 | #if spatial: |
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285 | #assert domain.geo_reference.xllcorner == xllcorner |
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286 | #assert domain.geo_reference.yllcorner == yllcorner |
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287 | #assert domain.geo_reference.zone == zone |
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288 | |
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289 | if verbose: |
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290 | print 'File_function data obtained from: %s' %filename |
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291 | print ' References:' |
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292 | #print ' Datum ....' #FIXME |
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293 | if spatial: |
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294 | print ' Lower left corner: [%f, %f]'\ |
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295 | %(xllcorner, yllcorner) |
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296 | print ' Start time: %f' %starttime |
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297 | |
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298 | |
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299 | #Produce values for desired data points at |
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300 | #each timestep |
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301 | |
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302 | quantities = {} |
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303 | for i, name in enumerate(quantity_names): |
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304 | quantities[name] = fid.variables[name][:] |
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305 | fid.close() |
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306 | |
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307 | |
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308 | from least_squares import Interpolation_function |
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309 | |
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310 | if not spatial: |
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311 | vertex_coordinates = triangles = interpolation_points = None |
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312 | |
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313 | |
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314 | return Interpolation_function(time, |
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315 | quantities, |
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316 | quantity_names, |
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317 | vertex_coordinates, |
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318 | triangles, |
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319 | interpolation_points, |
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320 | verbose = verbose) |
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321 | |
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322 | |
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323 | |
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324 | |
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325 | |
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326 | def multiple_replace(text, dictionary): |
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327 | """Multiple replace of words in text |
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328 | |
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329 | text: String to be modified |
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330 | dictionary: Mapping of words that are to be substituted |
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331 | |
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332 | Python Cookbook 3.14 page 88 and page 90 |
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333 | """ |
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334 | |
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335 | import re |
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336 | |
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337 | #Create a regular expression from all of the dictionary keys |
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338 | #matching only entire words |
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339 | regex = re.compile(r'\b'+ \ |
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340 | r'\b|\b'.join(map(re.escape, dictionary.keys()))+ \ |
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341 | r'\b' ) |
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342 | |
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343 | #For each match, lookup the corresponding value in the dictionary |
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344 | return regex.sub(lambda match: dictionary[match.group(0)], text) |
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345 | |
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346 | |
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347 | |
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348 | |
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349 | def apply_expression_to_dictionary(expression, dictionary):#dictionary): |
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350 | """Apply arbitrary expression to values of dictionary |
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351 | |
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352 | Given an expression in terms of the keys, replace key by the |
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353 | corresponding values and evaluate. |
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354 | |
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355 | |
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356 | expression: Arbitrary, e.g. arithmetric, expression relating keys |
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357 | from dictionary. |
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358 | |
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359 | dictionary: Mapping between symbols in expression and objects that |
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360 | will be evaluated by expression. |
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361 | Values in dictionary must support operators given in |
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362 | expression e.g. by overloading |
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363 | |
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364 | due to a limitation with Numeric, this can not evaluate 0/0 |
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365 | In general, the user can fix by adding 1e-30 to the numerator. |
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366 | SciPy core can handle this situation. |
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367 | """ |
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368 | |
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369 | import types |
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370 | import re |
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371 | |
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372 | assert isinstance(expression, basestring) |
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373 | assert type(dictionary) == types.DictType |
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374 | |
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375 | #Convert dictionary values to textual representations suitable for eval |
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376 | D = {} |
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377 | for key in dictionary: |
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378 | D[key] = 'dictionary["%s"]' %key |
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379 | |
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380 | #Perform substitution of variables |
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381 | expression = multiple_replace(expression, D) |
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382 | |
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383 | #Evaluate and return |
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384 | try: |
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385 | return eval(expression) |
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386 | except NameError, e: |
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387 | msg = 'Expression "%s" could not be evaluated: %s' %(expression, e) |
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388 | raise NameError, msg |
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389 | except ValueError, e: |
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390 | msg = 'Expression "%s" could not be evaluated: %s' %(expression, e) |
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391 | raise ValueError, msg |
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392 | |
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393 | |
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394 | |
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395 | |
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396 | #################################### |
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397 | ####OBSOLETE STUFF |
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398 | |
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399 | |
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400 | def angle(v): |
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401 | """Temporary Interface to new location""" |
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402 | |
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403 | import anuga.utilities.numerical_tools as NT |
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404 | |
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405 | msg = 'angle has moved from util.py. ' |
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406 | msg += 'Please use "from anuga.utilities.numerical_tools import angle"' |
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407 | warn(msg, DeprecationWarning) |
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408 | |
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409 | return NT.angle(v) |
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410 | |
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411 | def anglediff(v0, v1): |
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412 | """Temporary Interface to new location""" |
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413 | |
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414 | import anuga.utilities.numerical_tools as NT |
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415 | |
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416 | msg = 'anglediff has moved from util.py. ' |
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417 | msg += 'Please use "from anuga.utilities.numerical_tools import anglediff"' |
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418 | warn(msg, DeprecationWarning) |
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419 | |
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420 | return NT.anglediff(v0, v1) |
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421 | |
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422 | |
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423 | def mean(x): |
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424 | """Temporary Interface to new location""" |
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425 | |
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426 | import anuga.utilities.numerical_tools as NT |
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427 | |
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428 | msg = 'mean has moved from util.py. ' |
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429 | msg += 'Please use "from anuga.utilities.numerical_tools import mean"' |
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430 | warn(msg, DeprecationWarning) |
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431 | |
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432 | return NT.mean(x) |
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433 | |
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434 | def point_on_line(*args, **kwargs): |
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435 | """Temporary Interface to new location""" |
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436 | |
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437 | msg = 'point_on_line has moved from util.py. ' |
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438 | msg += 'Please use "from anuga.utilities.polygon import point_on_line"' |
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439 | warn(msg, DeprecationWarning) |
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440 | |
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441 | return utilities.polygon.point_on_line(*args, **kwargs) |
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442 | |
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443 | def inside_polygon(*args, **kwargs): |
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444 | """Temporary Interface to new location""" |
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445 | |
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446 | print 'inside_polygon has moved from util.py. ', |
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447 | print 'Please use "from anuga.utilities.polygon import inside_polygon"' |
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448 | |
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449 | return utilities.polygon.inside_polygon(*args, **kwargs) |
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450 | |
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451 | def outside_polygon(*args, **kwargs): |
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452 | """Temporary Interface to new location""" |
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453 | |
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454 | print 'outside_polygon has moved from util.py. ', |
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455 | print 'Please use "from anuga.utilities.polygon import outside_polygon"' |
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456 | |
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457 | return utilities.polygon.outside_polygon(*args, **kwargs) |
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458 | |
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459 | |
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460 | def separate_points_by_polygon(*args, **kwargs): |
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461 | """Temporary Interface to new location""" |
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462 | |
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463 | print 'separate_points_by_polygon has moved from util.py. ', |
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464 | print 'Please use "from anuga.utilities.polygon import separate_points_by_polygon"' |
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465 | |
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466 | return utilities.polygon.separate_points_by_polygon(*args, **kwargs) |
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467 | |
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468 | |
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469 | |
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470 | def read_polygon(*args, **kwargs): |
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471 | """Temporary Interface to new location""" |
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472 | |
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473 | print 'read_polygon has moved from util.py. ', |
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474 | print 'Please use "from anuga.utilities.polygon import read_polygon"' |
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475 | |
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476 | return utilities.polygon.read_polygon(*args, **kwargs) |
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477 | |
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478 | |
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479 | def populate_polygon(*args, **kwargs): |
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480 | """Temporary Interface to new location""" |
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481 | |
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482 | print 'populate_polygon has moved from util.py. ', |
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483 | print 'Please use "from anuga.utilities.polygon import populate_polygon"' |
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484 | |
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485 | return utilities.polygon.populate_polygon(*args, **kwargs) |
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486 | |
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487 | def read_xya(filename): |
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488 | """Read simple xya file, possibly with a header in the first line, just |
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489 | x y [attributes] |
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490 | separated by whitespace |
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491 | |
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492 | Format can be either ASCII or NetCDF |
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493 | |
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494 | Return list of points, list of attributes and |
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495 | attribute names if present otherwise None |
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496 | """ |
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497 | print "read_xya is obsolete. Use import_points_file from load_mesh.loadASCII" |
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498 | #FIXME: Probably obsoleted by similar function in load_ASCII |
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499 | #FIXME: Name read_data_points (or see 'load' in pylab) |
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500 | |
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501 | |
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502 | from load_mesh.loadASCII import import_points_file |
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503 | |
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504 | points_dict = import_points_file(filename) |
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505 | return points_dict['pointlist'], points_dict['attributelist'] |
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506 | |
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507 | |
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508 | |
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509 | |
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