1 | """ Classes to read an SWW file. |
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2 | """ |
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3 | |
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4 | from anuga.coordinate_transforms.geo_reference import Geo_reference |
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5 | from anuga.config import netcdf_mode_r, netcdf_mode_w, netcdf_mode_a |
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6 | from anuga.config import netcdf_float, netcdf_float32, netcdf_int |
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7 | from anuga.config import max_float |
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8 | from anuga.utilities.numerical_tools import ensure_numeric |
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9 | import anuga.utilities.log as log |
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10 | from Scientific.IO.NetCDF import NetCDFFile |
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11 | |
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12 | from sts import Write_sts |
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13 | |
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14 | from anuga.coordinate_transforms.geo_reference import \ |
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15 | ensure_geo_reference |
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16 | |
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17 | from file_utils import create_filename |
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18 | import numpy as num |
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19 | |
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20 | ## |
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21 | # @brief Generic class for storing output to e.g. visualisation or checkpointing |
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22 | class Data_format: |
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23 | """Generic interface to data formats |
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24 | """ |
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25 | |
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26 | ## |
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27 | # @brief Instantiate this instance. |
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28 | # @param domain |
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29 | # @param extension |
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30 | # @param mode The mode of the underlying file. |
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31 | def __init__(self, domain, extension, mode=netcdf_mode_w): |
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32 | assert mode[0] in ['r', 'w', 'a'], \ |
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33 | "Mode %s must be either:\n" % mode + \ |
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34 | " 'w' (write)\n" + \ |
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35 | " 'r' (read)\n" + \ |
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36 | " 'a' (append)" |
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37 | |
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38 | #Create filename |
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39 | self.filename = create_filename(domain.get_datadir(), |
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40 | domain.get_name(), extension) |
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41 | |
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42 | self.timestep = 0 |
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43 | self.domain = domain |
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44 | |
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45 | # Exclude ghosts in case this is a parallel domain |
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46 | self.number_of_nodes = domain.number_of_full_nodes |
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47 | self.number_of_volumes = domain.number_of_full_triangles |
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48 | #self.number_of_volumes = len(domain) |
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49 | |
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50 | #FIXME: Should we have a general set_precision function? |
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51 | |
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52 | |
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53 | class SWW_file(Data_format): |
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54 | """Interface to native NetCDF format (.sww) for storing model output |
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55 | |
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56 | There are two kinds of data |
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57 | |
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58 | 1: Constant data: Vertex coordinates and field values. Stored once |
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59 | 2: Variable data: Conserved quantities. Stored once per timestep. |
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60 | |
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61 | All data is assumed to reside at vertex locations. |
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62 | """ |
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63 | |
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64 | ## |
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65 | # @brief Instantiate this instance. |
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66 | # @param domain ?? |
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67 | # @param mode Mode of the underlying data file. |
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68 | # @param max_size ?? |
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69 | # @param recursion ?? |
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70 | # @note Prepare the underlying data file if mode starts with 'w'. |
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71 | def __init__(self, domain, |
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72 | mode=netcdf_mode_w, max_size=2000000000, recursion=False): |
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73 | from Scientific.IO.NetCDF import NetCDFFile |
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74 | |
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75 | self.precision = netcdf_float32 # Use single precision for quantities |
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76 | self.recursion = recursion |
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77 | self.mode = mode |
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78 | if hasattr(domain, 'max_size'): |
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79 | self.max_size = domain.max_size # File size max is 2Gig |
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80 | else: |
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81 | self.max_size = max_size |
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82 | if hasattr(domain, 'minimum_storable_height'): |
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83 | self.minimum_storable_height = domain.minimum_storable_height |
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84 | else: |
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85 | self.minimum_storable_height = default_minimum_storable_height |
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86 | |
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87 | # Call parent constructor |
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88 | Data_format.__init__(self, domain, 'sww', mode) |
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89 | |
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90 | # Get static and dynamic quantities from domain |
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91 | static_quantities = [] |
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92 | dynamic_quantities = [] |
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93 | |
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94 | for q in domain.quantities_to_be_stored: |
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95 | flag = domain.quantities_to_be_stored[q] |
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96 | |
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97 | msg = 'Quantity %s is requested to be stored ' % q |
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98 | msg += 'but it does not exist in domain.quantities' |
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99 | assert q in domain.quantities, msg |
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100 | |
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101 | assert flag in [1,2] |
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102 | if flag == 1: static_quantities.append(q) |
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103 | if flag == 2: dynamic_quantities.append(q) |
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104 | |
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105 | |
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106 | # NetCDF file definition |
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107 | fid = NetCDFFile(self.filename, mode) |
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108 | if mode[0] == 'w': |
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109 | description = 'Output from anuga.abstract_2d_finite_volumes ' \ |
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110 | 'suitable for plotting' |
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111 | |
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112 | self.writer = Write_sww(static_quantities, dynamic_quantities) |
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113 | self.writer.store_header(fid, |
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114 | domain.starttime, |
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115 | self.number_of_volumes, |
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116 | self.domain.number_of_full_nodes, |
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117 | description=description, |
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118 | smoothing=domain.smooth, |
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119 | order=domain.default_order, |
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120 | sww_precision=self.precision) |
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121 | |
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122 | # Extra optional information |
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123 | if hasattr(domain, 'texture'): |
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124 | fid.texture = domain.texture |
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125 | |
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126 | if domain.quantities_to_be_monitored is not None: |
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127 | fid.createDimension('singleton', 1) |
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128 | fid.createDimension('two', 2) |
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129 | |
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130 | poly = domain.monitor_polygon |
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131 | if poly is not None: |
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132 | N = len(poly) |
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133 | fid.createDimension('polygon_length', N) |
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134 | fid.createVariable('extrema.polygon', |
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135 | self.precision, |
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136 | ('polygon_length', 'two')) |
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137 | fid.variables['extrema.polygon'][:] = poly |
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138 | |
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139 | interval = domain.monitor_time_interval |
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140 | if interval is not None: |
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141 | fid.createVariable('extrema.time_interval', |
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142 | self.precision, |
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143 | ('two',)) |
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144 | fid.variables['extrema.time_interval'][:] = interval |
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145 | |
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146 | for q in domain.quantities_to_be_monitored: |
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147 | fid.createVariable(q + '.extrema', self.precision, |
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148 | ('numbers_in_range',)) |
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149 | fid.createVariable(q + '.min_location', self.precision, |
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150 | ('numbers_in_range',)) |
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151 | fid.createVariable(q + '.max_location', self.precision, |
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152 | ('numbers_in_range',)) |
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153 | fid.createVariable(q + '.min_time', self.precision, |
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154 | ('singleton',)) |
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155 | fid.createVariable(q + '.max_time', self.precision, |
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156 | ('singleton',)) |
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157 | |
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158 | fid.close() |
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159 | |
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160 | ## |
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161 | # @brief Store connectivity data into the underlying data file. |
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162 | def store_connectivity(self): |
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163 | """Store information about nodes, triangles and static quantities |
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164 | |
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165 | Writes x,y coordinates of triangles and their connectivity. |
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166 | |
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167 | Store also any quantity that has been identified as static. |
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168 | """ |
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169 | |
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170 | # FIXME: Change name to reflect the fact thta this function |
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171 | # stores both connectivity (triangulation) and static quantities |
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172 | |
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173 | from Scientific.IO.NetCDF import NetCDFFile |
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174 | |
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175 | domain = self.domain |
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176 | |
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177 | # append to the NetCDF file |
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178 | fid = NetCDFFile(self.filename, netcdf_mode_a) |
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179 | |
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180 | # Get X, Y from one (any) of the quantities |
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181 | Q = domain.quantities.values()[0] |
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182 | X,Y,_,V = Q.get_vertex_values(xy=True, precision=self.precision) |
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183 | |
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184 | # store the connectivity data |
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185 | points = num.concatenate((X[:,num.newaxis],Y[:,num.newaxis]), axis=1) |
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186 | self.writer.store_triangulation(fid, |
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187 | points, |
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188 | V.astype(num.float32), |
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189 | points_georeference=\ |
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190 | domain.geo_reference) |
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191 | |
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192 | |
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193 | # Get names of static quantities |
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194 | static_quantities = {} |
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195 | for name in self.writer.static_quantities: |
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196 | Q = domain.quantities[name] |
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197 | A, _ = Q.get_vertex_values(xy=False, |
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198 | precision=self.precision) |
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199 | static_quantities[name] = A |
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200 | |
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201 | # Store static quantities |
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202 | self.writer.store_static_quantities(fid, **static_quantities) |
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203 | |
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204 | fid.close() |
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205 | |
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206 | ## |
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207 | # @brief Store time and time dependent quantities |
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208 | # to the underlying data file. |
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209 | def store_timestep(self): |
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210 | """Store time and time dependent quantities |
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211 | """ |
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212 | |
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213 | from Scientific.IO.NetCDF import NetCDFFile |
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214 | import types |
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215 | from time import sleep |
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216 | from os import stat |
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217 | |
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218 | # Get NetCDF |
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219 | retries = 0 |
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220 | file_open = False |
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221 | while not file_open and retries < 10: |
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222 | try: |
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223 | # Open existing file |
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224 | fid = NetCDFFile(self.filename, netcdf_mode_a) |
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225 | except IOError: |
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226 | # This could happen if someone was reading the file. |
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227 | # In that case, wait a while and try again |
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228 | msg = 'Warning (store_timestep): File %s could not be opened' \ |
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229 | % self.filename |
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230 | msg += ' - trying step %s again' % self.domain.time |
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231 | log.critical(msg) |
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232 | retries += 1 |
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233 | sleep(1) |
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234 | else: |
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235 | file_open = True |
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236 | |
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237 | if not file_open: |
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238 | msg = 'File %s could not be opened for append' % self.filename |
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239 | raise DataFileNotOpenError, msg |
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240 | |
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241 | # Check to see if the file is already too big: |
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242 | time = fid.variables['time'] |
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243 | i = len(time) + 1 |
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244 | file_size = stat(self.filename)[6] |
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245 | file_size_increase = file_size / i |
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246 | if file_size + file_size_increase > self.max_size * 2**self.recursion: |
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247 | # In order to get the file name and start time correct, |
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248 | # I change the domain.filename and domain.starttime. |
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249 | # This is the only way to do this without changing |
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250 | # other modules (I think). |
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251 | |
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252 | # Write a filename addon that won't break the anuga viewers |
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253 | # (10.sww is bad) |
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254 | filename_ext = '_time_%s' % self.domain.time |
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255 | filename_ext = filename_ext.replace('.', '_') |
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256 | |
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257 | # Remember the old filename, then give domain a |
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258 | # name with the extension |
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259 | old_domain_filename = self.domain.get_name() |
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260 | if not self.recursion: |
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261 | self.domain.set_name(old_domain_filename + filename_ext) |
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262 | |
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263 | # Temporarily change the domain starttime to the current time |
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264 | old_domain_starttime = self.domain.starttime |
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265 | self.domain.starttime = self.domain.get_time() |
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266 | |
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267 | # Build a new data_structure. |
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268 | next_data_structure = SWW_file(self.domain, mode=self.mode, |
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269 | max_size=self.max_size, |
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270 | recursion=self.recursion+1) |
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271 | if not self.recursion: |
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272 | log.critical(' file_size = %s' % file_size) |
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273 | log.critical(' saving file to %s' |
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274 | % next_data_structure.filename) |
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275 | |
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276 | # Set up the new data_structure |
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277 | self.domain.writer = next_data_structure |
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278 | |
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279 | # Store connectivity and first timestep |
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280 | next_data_structure.store_connectivity() |
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281 | next_data_structure.store_timestep() |
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282 | fid.sync() |
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283 | fid.close() |
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284 | |
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285 | # Restore the old starttime and filename |
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286 | self.domain.starttime = old_domain_starttime |
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287 | self.domain.set_name(old_domain_filename) |
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288 | else: |
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289 | self.recursion = False |
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290 | domain = self.domain |
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291 | |
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292 | # Get the variables |
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293 | time = fid.variables['time'] |
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294 | i = len(time) |
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295 | |
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296 | if 'stage' in self.writer.dynamic_quantities: |
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297 | # Select only those values for stage, |
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298 | # xmomentum and ymomentum (if stored) where |
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299 | # depth exceeds minimum_storable_height |
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300 | # |
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301 | # In this branch it is assumed that elevation |
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302 | # is also available as a quantity |
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303 | |
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304 | Q = domain.quantities['stage'] |
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305 | w, _ = Q.get_vertex_values(xy=False) |
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306 | |
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307 | Q = domain.quantities['elevation'] |
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308 | z, _ = Q.get_vertex_values(xy=False) |
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309 | |
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310 | storable_indices = (w-z >= self.minimum_storable_height) |
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311 | else: |
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312 | # Very unlikely branch |
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313 | storable_indices = None # This means take all |
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314 | |
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315 | |
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316 | # Now store dynamic quantities |
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317 | dynamic_quantities = {} |
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318 | for name in self.writer.dynamic_quantities: |
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319 | netcdf_array = fid.variables[name] |
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320 | |
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321 | Q = domain.quantities[name] |
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322 | A, _ = Q.get_vertex_values(xy=False, |
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323 | precision=self.precision) |
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324 | |
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325 | if storable_indices is not None: |
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326 | if name == 'stage': |
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327 | A = num.choose(storable_indices, (z, A)) |
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328 | |
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329 | if name in ['xmomentum', 'ymomentum']: |
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330 | # Get xmomentum where depth exceeds |
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331 | # minimum_storable_height |
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332 | |
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333 | # Define a zero vector of same size and type as A |
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334 | # for use with momenta |
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335 | null = num.zeros(num.size(A), A.dtype.char) |
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336 | A = num.choose(storable_indices, (null, A)) |
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337 | |
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338 | dynamic_quantities[name] = A |
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339 | |
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340 | |
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341 | # Store dynamic quantities |
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342 | self.writer.store_quantities(fid, |
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343 | time=self.domain.time, |
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344 | sww_precision=self.precision, |
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345 | **dynamic_quantities) |
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346 | |
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347 | |
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348 | # Update extrema if requested |
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349 | domain = self.domain |
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350 | if domain.quantities_to_be_monitored is not None: |
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351 | for q, info in domain.quantities_to_be_monitored.items(): |
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352 | if info['min'] is not None: |
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353 | fid.variables[q + '.extrema'][0] = info['min'] |
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354 | fid.variables[q + '.min_location'][:] = \ |
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355 | info['min_location'] |
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356 | fid.variables[q + '.min_time'][0] = info['min_time'] |
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357 | |
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358 | if info['max'] is not None: |
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359 | fid.variables[q + '.extrema'][1] = info['max'] |
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360 | fid.variables[q + '.max_location'][:] = \ |
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361 | info['max_location'] |
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362 | fid.variables[q + '.max_time'][0] = info['max_time'] |
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363 | |
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364 | # Flush and close |
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365 | fid.sync() |
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366 | fid.close() |
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367 | |
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368 | |
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369 | ## |
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370 | # @brief Class to open an sww file so that domain can be populated with quantity values |
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371 | class Read_sww: |
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372 | |
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373 | def __init__(self, source): |
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374 | """The source parameter is assumed to be a NetCDF sww file. |
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375 | """ |
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376 | |
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377 | self.source = source |
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378 | |
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379 | self.frame_number = 0 |
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380 | |
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381 | fin = NetCDFFile(self.source, 'r') |
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382 | |
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383 | self.time = num.array(fin.variables['time'], num.float) |
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384 | self.last_frame_number = self.time.shape[0] - 1 |
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385 | |
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386 | self.frames = num.arange(self.last_frame_number+1) |
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387 | |
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388 | fin.close() |
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389 | |
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390 | self.read_mesh() |
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391 | |
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392 | self.quantities = {} |
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393 | |
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394 | self.read_quantities() |
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395 | |
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396 | |
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397 | def read_mesh(self): |
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398 | """ Read and store the mesh data contained within this sww file. |
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399 | """ |
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400 | fin = NetCDFFile(self.source, 'r') |
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401 | |
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402 | self.vertices = num.array(fin.variables['volumes'], num.int) |
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403 | |
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404 | self.x = x = num.array(fin.variables['x'], num.float) |
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405 | self.y = y = num.array(fin.variables['y'], num.float) |
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406 | |
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407 | assert len(self.x) == len(self.y) |
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408 | |
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409 | self.xmin = num.min(x) |
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410 | self.xmax = num.max(x) |
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411 | self.ymin = num.min(y) |
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412 | self.ymax = num.max(y) |
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413 | |
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414 | |
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415 | fin.close() |
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416 | |
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417 | def read_quantities(self, frame_number=0): |
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418 | """ |
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419 | Read the quantities contained in this file. |
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420 | frame_number is the time index to load. |
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421 | """ |
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422 | assert frame_number >= 0 and frame_number <= self.last_frame_number |
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423 | |
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424 | self.frame_number = frame_number |
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425 | |
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426 | M = len(self.x)/3 |
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427 | |
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428 | fin = NetCDFFile(self.source, 'r') |
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429 | |
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430 | for q in filter(lambda n:n != 'x' and n != 'y' and n != 'time' and n != 'volumes' and \ |
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431 | '_range' not in n, \ |
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432 | fin.variables.keys()): |
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433 | if len(fin.variables[q].shape) == 1: # Not a time-varying quantity |
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434 | self.quantities[q] = num.ravel(num.array(fin.variables[q], num.float)).reshape(M,3) |
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435 | else: # Time-varying, get the current timestep data |
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436 | self.quantities[q] = num.array(fin.variables[q][self.frame_number], num.float).reshape(M,3) |
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437 | fin.close() |
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438 | return self.quantities |
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439 | |
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440 | def get_bounds(self): |
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441 | """ |
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442 | Get the bounding rect around the mesh. |
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443 | """ |
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444 | return [self.xmin, self.xmax, self.ymin, self.ymax] |
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445 | |
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446 | def get_last_frame_number(self): |
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447 | """ |
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448 | Return the last loaded frame index. |
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449 | """ |
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450 | return self.last_frame_number |
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451 | |
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452 | def get_time(self): |
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453 | """ |
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454 | Get time at the current frame num, in secs. |
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455 | """ |
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456 | return self.time[self.frame_number] |
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457 | |
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458 | |
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459 | class Write_sww(Write_sts): |
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460 | """ |
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461 | A class to write an SWW file. |
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462 | |
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463 | It is domain agnostic, and requires all the data to be fed in |
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464 | manually. |
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465 | """ |
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466 | |
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467 | def __init__(self, static_quantities, dynamic_quantities): |
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468 | """Initialise Write_sww with two list af quantity names: |
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469 | |
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470 | static_quantities (e.g. elevation or friction): |
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471 | Stored once at the beginning of the simulation in a 1D array |
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472 | of length number_of_points |
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473 | dynamic_quantities (e.g stage): |
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474 | Stored every timestep in a 2D array with |
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475 | dimensions number_of_points X number_of_timesteps |
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476 | |
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477 | """ |
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478 | self.static_quantities = static_quantities |
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479 | self.dynamic_quantities = dynamic_quantities |
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480 | |
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481 | |
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482 | def store_header(self, |
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483 | outfile, |
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484 | times, |
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485 | number_of_volumes, |
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486 | number_of_points, |
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487 | description='Generated by ANUGA', |
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488 | smoothing=True, |
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489 | order=1, |
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490 | sww_precision=netcdf_float32, |
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491 | verbose=False): |
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492 | """Write an SWW file header. |
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493 | |
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494 | Writes the first section of the .sww file. |
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495 | |
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496 | outfile - the open file that will be written |
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497 | times - A list of the time slice times OR a start time |
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498 | Note, if a list is given the info will be made relative. |
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499 | number_of_volumes - the number of triangles |
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500 | number_of_points - the number of vertices in the mesh |
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501 | """ |
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502 | |
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503 | from anuga.abstract_2d_finite_volumes.util \ |
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504 | import get_revision_number |
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505 | |
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506 | outfile.institution = 'Geoscience Australia' |
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507 | outfile.description = description |
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508 | |
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509 | # For sww compatibility |
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510 | if smoothing is True: |
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511 | # Smoothing to be depreciated |
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512 | outfile.smoothing = 'Yes' |
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513 | outfile.vertices_are_stored_uniquely = 'False' |
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514 | else: |
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515 | # Smoothing to be depreciated |
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516 | outfile.smoothing = 'No' |
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517 | outfile.vertices_are_stored_uniquely = 'True' |
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518 | outfile.order = order |
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519 | |
---|
520 | try: |
---|
521 | revision_number = get_revision_number() |
---|
522 | except: |
---|
523 | # This will be triggered if the system cannot get the SVN |
---|
524 | # revision number. |
---|
525 | revision_number = None |
---|
526 | # Allow None to be stored as a string |
---|
527 | outfile.revision_number = str(revision_number) |
---|
528 | |
---|
529 | # This is being used to seperate one number from a list. |
---|
530 | # what it is actually doing is sorting lists from numeric arrays. |
---|
531 | if isinstance(times, (list, num.ndarray)): |
---|
532 | number_of_times = len(times) |
---|
533 | times = ensure_numeric(times) |
---|
534 | if number_of_times == 0: |
---|
535 | starttime = 0 |
---|
536 | else: |
---|
537 | starttime = times[0] |
---|
538 | times = times - starttime #Store relative times |
---|
539 | else: |
---|
540 | number_of_times = 0 |
---|
541 | starttime = times |
---|
542 | |
---|
543 | |
---|
544 | outfile.starttime = starttime |
---|
545 | |
---|
546 | # dimension definitions |
---|
547 | outfile.createDimension('number_of_volumes', number_of_volumes) |
---|
548 | outfile.createDimension('number_of_vertices', 3) |
---|
549 | outfile.createDimension('numbers_in_range', 2) |
---|
550 | |
---|
551 | if smoothing is True: |
---|
552 | outfile.createDimension('number_of_points', number_of_points) |
---|
553 | # FIXME(Ole): This will cause sww files for parallel domains to |
---|
554 | # have ghost nodes stored (but not used by triangles). |
---|
555 | # To clean this up, we have to change get_vertex_values and |
---|
556 | # friends in quantity.py (but I can't be bothered right now) |
---|
557 | else: |
---|
558 | outfile.createDimension('number_of_points', 3*number_of_volumes) |
---|
559 | |
---|
560 | outfile.createDimension('number_of_timesteps', number_of_times) |
---|
561 | |
---|
562 | # variable definitions |
---|
563 | outfile.createVariable('x', sww_precision, ('number_of_points',)) |
---|
564 | outfile.createVariable('y', sww_precision, ('number_of_points',)) |
---|
565 | |
---|
566 | outfile.createVariable('volumes', netcdf_int, ('number_of_volumes', |
---|
567 | 'number_of_vertices')) |
---|
568 | |
---|
569 | |
---|
570 | for q in self.static_quantities: |
---|
571 | |
---|
572 | outfile.createVariable(q, sww_precision, |
---|
573 | ('number_of_points',)) |
---|
574 | |
---|
575 | outfile.createVariable(q + Write_sww.RANGE, sww_precision, |
---|
576 | ('numbers_in_range',)) |
---|
577 | |
---|
578 | # Initialise ranges with small and large sentinels. |
---|
579 | # If this was in pure Python we could have used None sensibly |
---|
580 | outfile.variables[q+Write_sww.RANGE][0] = max_float # Min |
---|
581 | outfile.variables[q+Write_sww.RANGE][1] = -max_float # Max |
---|
582 | |
---|
583 | |
---|
584 | self.write_dynamic_quantities(outfile, self.dynamic_quantities, times) |
---|
585 | |
---|
586 | |
---|
587 | |
---|
588 | def store_triangulation(self, |
---|
589 | outfile, |
---|
590 | points_utm, |
---|
591 | volumes, |
---|
592 | zone=None, |
---|
593 | new_origin=None, |
---|
594 | points_georeference=None, |
---|
595 | verbose=False): |
---|
596 | """ |
---|
597 | Store triangulation data in the underlying file. |
---|
598 | |
---|
599 | Stores the points and triangle indices in the sww file |
---|
600 | |
---|
601 | outfile Open handle to underlying file. |
---|
602 | |
---|
603 | new_origin georeference that the points can be set to. |
---|
604 | |
---|
605 | points_georeference The georeference of the points_utm. |
---|
606 | |
---|
607 | verbose True if this function is to be verbose. |
---|
608 | |
---|
609 | new_origin - qa georeference that the points can be set to. (Maybe |
---|
610 | do this before calling this function.) |
---|
611 | |
---|
612 | points_utm - currently a list or array of the points in UTM. |
---|
613 | points_georeference - the georeference of the points_utm |
---|
614 | |
---|
615 | How about passing new_origin and current_origin. |
---|
616 | If you get both, do a convertion from the old to the new. |
---|
617 | |
---|
618 | If you only get new_origin, the points are absolute, |
---|
619 | convert to relative |
---|
620 | |
---|
621 | if you only get the current_origin the points are relative, store |
---|
622 | as relative. |
---|
623 | |
---|
624 | if you get no georefs create a new georef based on the minimums of |
---|
625 | points_utm. (Another option would be to default to absolute) |
---|
626 | |
---|
627 | Yes, and this is done in another part of the code. |
---|
628 | Probably geospatial. |
---|
629 | |
---|
630 | If you don't supply either geo_refs, then supply a zone. If not |
---|
631 | the default zone will be used. |
---|
632 | |
---|
633 | precon: |
---|
634 | header has been called. |
---|
635 | """ |
---|
636 | |
---|
637 | number_of_points = len(points_utm) |
---|
638 | volumes = num.array(volumes) |
---|
639 | points_utm = num.array(points_utm) |
---|
640 | |
---|
641 | # Given the two geo_refs and the points, do the stuff |
---|
642 | # described in the method header |
---|
643 | # if this is needed else where, pull out as a function |
---|
644 | points_georeference = ensure_geo_reference(points_georeference) |
---|
645 | new_origin = ensure_geo_reference(new_origin) |
---|
646 | if new_origin is None and points_georeference is not None: |
---|
647 | points = points_utm |
---|
648 | geo_ref = points_georeference |
---|
649 | else: |
---|
650 | if new_origin is None: |
---|
651 | new_origin = Geo_reference(zone, min(points_utm[:,0]), |
---|
652 | min(points_utm[:,1])) |
---|
653 | points = new_origin.change_points_geo_ref(points_utm, |
---|
654 | points_georeference) |
---|
655 | geo_ref = new_origin |
---|
656 | |
---|
657 | # At this stage I need a georef and points |
---|
658 | # the points are relative to the georef |
---|
659 | geo_ref.write_NetCDF(outfile) |
---|
660 | |
---|
661 | # This will put the geo ref in the middle |
---|
662 | #geo_ref = Geo_reference(refzone,(max(x)+min(x))/2.0,(max(x)+min(y))/2.) |
---|
663 | |
---|
664 | x = points[:,0] |
---|
665 | y = points[:,1] |
---|
666 | |
---|
667 | if verbose: |
---|
668 | log.critical('------------------------------------------------') |
---|
669 | log.critical('More Statistics:') |
---|
670 | log.critical(' Extent (/lon):') |
---|
671 | log.critical(' x in [%f, %f], len(lat) == %d' |
---|
672 | % (min(x), max(x), len(x))) |
---|
673 | log.critical(' y in [%f, %f], len(lon) == %d' |
---|
674 | % (min(y), max(y), len(y))) |
---|
675 | #log.critical(' z in [%f, %f], len(z) == %d' |
---|
676 | # % (min(elevation), max(elevation), len(elevation))) |
---|
677 | log.critical('geo_ref: %s' % str(geo_ref)) |
---|
678 | log.critical('------------------------------------------------') |
---|
679 | |
---|
680 | outfile.variables['x'][:] = points[:,0] #- geo_ref.get_xllcorner() |
---|
681 | outfile.variables['y'][:] = points[:,1] #- geo_ref.get_yllcorner() |
---|
682 | outfile.variables['volumes'][:] = volumes.astype(num.int32) #On Opteron 64 |
---|
683 | |
---|
684 | |
---|
685 | def store_static_quantities(self, |
---|
686 | outfile, |
---|
687 | sww_precision=num.float32, |
---|
688 | verbose=False, |
---|
689 | **quant): |
---|
690 | """ |
---|
691 | Write the static quantity info. |
---|
692 | |
---|
693 | **quant is extra keyword arguments passed in. These must be |
---|
694 | the numpy arrays to be stored in the sww file at each timestep. |
---|
695 | |
---|
696 | The argument sww_precision allows for storing as either |
---|
697 | * single precision (default): num.float32 |
---|
698 | * double precision: num.float64 or num.float |
---|
699 | |
---|
700 | Precondition: |
---|
701 | store_triangulation and |
---|
702 | store_header have been called. |
---|
703 | """ |
---|
704 | |
---|
705 | # The dictionary quant must contain numpy arrays for each name. |
---|
706 | # These will typically be quantities from Domain such as friction |
---|
707 | # |
---|
708 | # Arrays not listed in static_quantitiues will be ignored, silently. |
---|
709 | # |
---|
710 | # This method will also write the ranges for each quantity, |
---|
711 | # e.g. stage_range, xmomentum_range and ymomentum_range |
---|
712 | for q in self.static_quantities: |
---|
713 | if not quant.has_key(q): |
---|
714 | msg = 'Values for quantity %s was not specified in ' % q |
---|
715 | msg += 'store_quantities so they cannot be stored.' |
---|
716 | raise NewQuantity, msg |
---|
717 | else: |
---|
718 | q_values = ensure_numeric(quant[q]) |
---|
719 | |
---|
720 | x = q_values.astype(sww_precision) |
---|
721 | outfile.variables[q][:] = x |
---|
722 | |
---|
723 | # This populates the _range values |
---|
724 | outfile.variables[q + Write_sww.RANGE][0] = num.min(x) |
---|
725 | outfile.variables[q + Write_sww.RANGE][1] = num.max(x) |
---|
726 | |
---|
727 | # FIXME: Hack for backwards compatibility with old viewer |
---|
728 | #if 'elevation' in self.static_quantities: |
---|
729 | # outfile.variables['z'][:] = outfile.variables['elevation'][:] |
---|
730 | |
---|
731 | |
---|
732 | |
---|
733 | |
---|
734 | |
---|
735 | def store_quantities(self, |
---|
736 | outfile, |
---|
737 | sww_precision=num.float32, |
---|
738 | slice_index=None, |
---|
739 | time=None, |
---|
740 | verbose=False, |
---|
741 | **quant): |
---|
742 | """ |
---|
743 | Write the quantity info at each timestep. |
---|
744 | |
---|
745 | **quant is extra keyword arguments passed in. These must be |
---|
746 | the numpy arrays to be stored in the sww file at each timestep. |
---|
747 | |
---|
748 | if the time array is already been built, use the slice_index |
---|
749 | to specify the index. |
---|
750 | |
---|
751 | Otherwise, use time to increase the time dimension |
---|
752 | |
---|
753 | Maybe make this general, but the viewer assumes these quantities, |
---|
754 | so maybe we don't want it general - unless the viewer is general |
---|
755 | |
---|
756 | The argument sww_precision allows for storing as either |
---|
757 | * single precision (default): num.float32 |
---|
758 | * double precision: num.float64 or num.float |
---|
759 | |
---|
760 | Precondition: |
---|
761 | store_triangulation and |
---|
762 | store_header have been called. |
---|
763 | """ |
---|
764 | |
---|
765 | if time is not None: |
---|
766 | file_time = outfile.variables['time'] |
---|
767 | slice_index = len(file_time) |
---|
768 | file_time[slice_index] = time |
---|
769 | else: |
---|
770 | slice_index = int(slice_index) # Has to be cast in case it was numpy.int |
---|
771 | |
---|
772 | # Write the named dynamic quantities |
---|
773 | # The dictionary quant must contain numpy arrays for each name. |
---|
774 | # These will typically be the conserved quantities from Domain |
---|
775 | # (Typically stage, xmomentum, ymomentum). |
---|
776 | # |
---|
777 | # Arrays not listed in dynamic_quantitiues will be ignored, silently. |
---|
778 | # |
---|
779 | # This method will also write the ranges for each quantity, |
---|
780 | # e.g. stage_range, xmomentum_range and ymomentum_range |
---|
781 | for q in self.dynamic_quantities: |
---|
782 | if not quant.has_key(q): |
---|
783 | msg = 'Values for quantity %s was not specified in ' % q |
---|
784 | msg += 'store_quantities so they cannot be stored.' |
---|
785 | raise NewQuantity, msg |
---|
786 | else: |
---|
787 | q_values = ensure_numeric(quant[q]) |
---|
788 | |
---|
789 | x = q_values.astype(sww_precision) |
---|
790 | outfile.variables[q][slice_index] = x |
---|
791 | |
---|
792 | # This updates the _range values |
---|
793 | q_range = outfile.variables[q + Write_sww.RANGE][:] |
---|
794 | q_values_min = num.min(q_values) |
---|
795 | if q_values_min < q_range[0]: |
---|
796 | outfile.variables[q + Write_sww.RANGE][0] = q_values_min |
---|
797 | q_values_max = num.max(q_values) |
---|
798 | if q_values_max > q_range[1]: |
---|
799 | outfile.variables[q + Write_sww.RANGE][1] = q_values_max |
---|
800 | |
---|
801 | ## |
---|
802 | # @brief Print the quantities in the underlying file. |
---|
803 | # @param outfile UNUSED. |
---|
804 | def verbose_quantities(self, outfile): |
---|
805 | log.critical('------------------------------------------------') |
---|
806 | log.critical('More Statistics:') |
---|
807 | for q in self.dynamic_quantities: |
---|
808 | log.critical(' %s in [%f, %f]' |
---|
809 | % (q, outfile.variables[q+Write_sww.RANGE][0], |
---|
810 | outfile.variables[q+Write_sww.RANGE][1])) |
---|
811 | log.critical('------------------------------------------------') |
---|
812 | |
---|
813 | |
---|
814 | |
---|
815 | |
---|
816 | def extent_sww(file_name): |
---|
817 | """Read in an sww file, then get its extents |
---|
818 | |
---|
819 | Input: |
---|
820 | file_name - the sww file |
---|
821 | |
---|
822 | Output: |
---|
823 | A list: [min(x),max(x),min(y),max(y),min(stage.flat),max(stage.flat)] |
---|
824 | """ |
---|
825 | |
---|
826 | from Scientific.IO.NetCDF import NetCDFFile |
---|
827 | |
---|
828 | #Get NetCDF |
---|
829 | fid = NetCDFFile(file_name, netcdf_mode_r) |
---|
830 | |
---|
831 | # Get the variables |
---|
832 | x = fid.variables['x'][:] |
---|
833 | y = fid.variables['y'][:] |
---|
834 | stage = fid.variables['stage'][:] |
---|
835 | |
---|
836 | fid.close() |
---|
837 | |
---|
838 | return [min(x), max(x), min(y), max(y), num.min(stage), num.max(stage)] |
---|
839 | |
---|
840 | |
---|
841 | def load_sww_as_domain(filename, boundary=None, t=None, |
---|
842 | fail_if_NaN=True, NaN_filler=0, |
---|
843 | verbose=False, very_verbose=False): |
---|
844 | """ |
---|
845 | Load an sww file into a domain. |
---|
846 | |
---|
847 | Usage: domain = load_sww_as_domain('file.sww', |
---|
848 | t=time (default = last time in file)) |
---|
849 | |
---|
850 | Boundary is not recommended if domain.smooth is not selected, as it |
---|
851 | uses unique coordinates, but not unique boundaries. This means that |
---|
852 | the boundary file will not be compatable with the coordinates, and will |
---|
853 | give a different final boundary, or crash. |
---|
854 | """ |
---|
855 | |
---|
856 | from Scientific.IO.NetCDF import NetCDFFile |
---|
857 | from anuga.shallow_water.shallow_water_domain import Domain |
---|
858 | |
---|
859 | # initialise NaN. |
---|
860 | NaN = 9.969209968386869e+036 |
---|
861 | |
---|
862 | if verbose: log.critical('Reading from %s' % filename) |
---|
863 | |
---|
864 | fid = NetCDFFile(filename, netcdf_mode_r) # Open existing file for read |
---|
865 | time = fid.variables['time'] # Timesteps |
---|
866 | if t is None: |
---|
867 | t = time[-1] |
---|
868 | time_interp = get_time_interp(time,t) |
---|
869 | |
---|
870 | # Get the variables as numeric arrays |
---|
871 | x = fid.variables['x'][:] # x-coordinates of vertices |
---|
872 | y = fid.variables['y'][:] # y-coordinates of vertices |
---|
873 | elevation = fid.variables['elevation'] # Elevation |
---|
874 | stage = fid.variables['stage'] # Water level |
---|
875 | xmomentum = fid.variables['xmomentum'] # Momentum in the x-direction |
---|
876 | ymomentum = fid.variables['ymomentum'] # Momentum in the y-direction |
---|
877 | |
---|
878 | starttime = fid.starttime[0] |
---|
879 | volumes = fid.variables['volumes'][:] # Connectivity |
---|
880 | coordinates = num.transpose(num.asarray([x.tolist(), y.tolist()])) |
---|
881 | # FIXME (Ole): Something like this might be better: |
---|
882 | # concatenate((x, y), axis=1) |
---|
883 | # or concatenate((x[:,num.newaxis], x[:,num.newaxis]), axis=1) |
---|
884 | |
---|
885 | conserved_quantities = [] |
---|
886 | interpolated_quantities = {} |
---|
887 | other_quantities = [] |
---|
888 | |
---|
889 | # get geo_reference |
---|
890 | try: # sww files don't have to have a geo_ref |
---|
891 | geo_reference = Geo_reference(NetCDFObject=fid) |
---|
892 | except: # AttributeError, e: |
---|
893 | geo_reference = None |
---|
894 | |
---|
895 | if verbose: log.critical(' getting quantities') |
---|
896 | |
---|
897 | for quantity in fid.variables.keys(): |
---|
898 | dimensions = fid.variables[quantity].dimensions |
---|
899 | if 'number_of_timesteps' in dimensions: |
---|
900 | conserved_quantities.append(quantity) |
---|
901 | interpolated_quantities[quantity] = \ |
---|
902 | interpolated_quantity(fid.variables[quantity][:], time_interp) |
---|
903 | else: |
---|
904 | other_quantities.append(quantity) |
---|
905 | |
---|
906 | other_quantities.remove('x') |
---|
907 | other_quantities.remove('y') |
---|
908 | #other_quantities.remove('z') |
---|
909 | other_quantities.remove('volumes') |
---|
910 | try: |
---|
911 | other_quantities.remove('stage_range') |
---|
912 | other_quantities.remove('xmomentum_range') |
---|
913 | other_quantities.remove('ymomentum_range') |
---|
914 | other_quantities.remove('elevation_range') |
---|
915 | except: |
---|
916 | pass |
---|
917 | |
---|
918 | conserved_quantities.remove('time') |
---|
919 | |
---|
920 | if verbose: log.critical(' building domain') |
---|
921 | |
---|
922 | # From domain.Domain: |
---|
923 | # domain = Domain(coordinates, volumes,\ |
---|
924 | # conserved_quantities = conserved_quantities,\ |
---|
925 | # other_quantities = other_quantities,zone=zone,\ |
---|
926 | # xllcorner=xllcorner, yllcorner=yllcorner) |
---|
927 | |
---|
928 | # From shallow_water.Domain: |
---|
929 | coordinates = coordinates.tolist() |
---|
930 | volumes = volumes.tolist() |
---|
931 | # FIXME:should this be in mesh? (peter row) |
---|
932 | if fid.smoothing == 'Yes': |
---|
933 | unique = False |
---|
934 | else: |
---|
935 | unique = True |
---|
936 | if unique: |
---|
937 | coordinates, volumes, boundary = weed(coordinates, volumes,boundary) |
---|
938 | |
---|
939 | |
---|
940 | |
---|
941 | try: |
---|
942 | domain = Domain(coordinates, volumes, boundary) |
---|
943 | except AssertionError, e: |
---|
944 | fid.close() |
---|
945 | msg = 'Domain could not be created: %s. ' \ |
---|
946 | 'Perhaps use "fail_if_NaN=False and NaN_filler = ..."' % e |
---|
947 | raise DataDomainError, msg |
---|
948 | |
---|
949 | if not boundary is None: |
---|
950 | domain.boundary = boundary |
---|
951 | |
---|
952 | domain.geo_reference = geo_reference |
---|
953 | |
---|
954 | domain.starttime = float(starttime) + float(t) |
---|
955 | domain.time = 0.0 |
---|
956 | |
---|
957 | for quantity in other_quantities: |
---|
958 | try: |
---|
959 | NaN = fid.variables[quantity].missing_value |
---|
960 | except: |
---|
961 | pass # quantity has no missing_value number |
---|
962 | X = fid.variables[quantity][:] |
---|
963 | if very_verbose: |
---|
964 | log.critical(' %s' % str(quantity)) |
---|
965 | log.critical(' NaN = %s' % str(NaN)) |
---|
966 | log.critical(' max(X)') |
---|
967 | log.critical(' %s' % str(max(X))) |
---|
968 | log.critical(' max(X)==NaN') |
---|
969 | log.critical(' %s' % str(max(X)==NaN)) |
---|
970 | log.critical('') |
---|
971 | if max(X) == NaN or min(X) == NaN: |
---|
972 | if fail_if_NaN: |
---|
973 | msg = 'quantity "%s" contains no_data entry' % quantity |
---|
974 | raise DataMissingValuesError, msg |
---|
975 | else: |
---|
976 | data = (X != NaN) |
---|
977 | X = (X*data) + (data==0)*NaN_filler |
---|
978 | if unique: |
---|
979 | X = num.resize(X, (len(X)/3, 3)) |
---|
980 | domain.set_quantity(quantity, X) |
---|
981 | # |
---|
982 | for quantity in conserved_quantities: |
---|
983 | try: |
---|
984 | NaN = fid.variables[quantity].missing_value |
---|
985 | except: |
---|
986 | pass # quantity has no missing_value number |
---|
987 | X = interpolated_quantities[quantity] |
---|
988 | if very_verbose: |
---|
989 | log.critical(' %s' % str(quantity)) |
---|
990 | log.critical(' NaN = %s' % str(NaN)) |
---|
991 | log.critical(' max(X)') |
---|
992 | log.critical(' %s' % str(max(X))) |
---|
993 | log.critical(' max(X)==NaN') |
---|
994 | log.critical(' %s' % str(max(X)==NaN)) |
---|
995 | log.critical('') |
---|
996 | if max(X) == NaN or min(X) == NaN: |
---|
997 | if fail_if_NaN: |
---|
998 | msg = 'quantity "%s" contains no_data entry' % quantity |
---|
999 | raise DataMissingValuesError, msg |
---|
1000 | else: |
---|
1001 | data = (X != NaN) |
---|
1002 | X = (X*data) + (data==0)*NaN_filler |
---|
1003 | if unique: |
---|
1004 | X = num.resize(X, (X.shape[0]/3, 3)) |
---|
1005 | domain.set_quantity(quantity, X) |
---|
1006 | |
---|
1007 | fid.close() |
---|
1008 | |
---|
1009 | return domain |
---|
1010 | |
---|
1011 | |
---|
1012 | def get_mesh_and_quantities_from_file(filename, |
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1013 | quantities=None, |
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1014 | verbose=False): |
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1015 | """Get and rebuild mesh structure and associated quantities from sww file |
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1016 | |
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1017 | Input: |
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1018 | filename - Name os sww file |
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1019 | quantities - Names of quantities to load |
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1020 | |
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1021 | Output: |
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1022 | mesh - instance of class Interpolate |
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1023 | (including mesh and interpolation functionality) |
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1024 | quantities - arrays with quantity values at each mesh node |
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1025 | time - vector of stored timesteps |
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1026 | |
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1027 | This function is used by e.g.: |
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1028 | get_interpolated_quantities_at_polyline_midpoints |
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1029 | """ |
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1030 | |
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1031 | # FIXME (Ole): Maybe refactor filefunction using this more fundamental code. |
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1032 | |
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1033 | import types |
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1034 | from Scientific.IO.NetCDF import NetCDFFile |
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1035 | from anuga.abstract_2d_finite_volumes.neighbour_mesh import Mesh |
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1036 | |
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1037 | if verbose: log.critical('Reading from %s' % filename) |
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1038 | |
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1039 | fid = NetCDFFile(filename, netcdf_mode_r) # Open existing file for read |
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1040 | time = fid.variables['time'][:] # Time vector |
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1041 | time += fid.starttime[0] |
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1042 | |
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1043 | # Get the variables as numeric arrays |
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1044 | x = fid.variables['x'][:] # x-coordinates of nodes |
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1045 | y = fid.variables['y'][:] # y-coordinates of nodes |
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1046 | elevation = fid.variables['elevation'][:] # Elevation |
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1047 | stage = fid.variables['stage'][:] # Water level |
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1048 | xmomentum = fid.variables['xmomentum'][:] # Momentum in the x-direction |
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1049 | ymomentum = fid.variables['ymomentum'][:] # Momentum in the y-direction |
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1050 | |
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1051 | # Mesh (nodes (Mx2), triangles (Nx3)) |
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1052 | nodes = num.concatenate((x[:,num.newaxis], y[:,num.newaxis]), axis=1) |
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1053 | triangles = fid.variables['volumes'][:] |
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1054 | |
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1055 | # Get geo_reference |
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1056 | try: |
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1057 | geo_reference = Geo_reference(NetCDFObject=fid) |
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1058 | except: #AttributeError, e: |
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1059 | # Sww files don't have to have a geo_ref |
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1060 | geo_reference = None |
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1061 | |
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1062 | if verbose: log.critical(' building mesh from sww file %s' % filename) |
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1063 | |
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1064 | boundary = None |
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1065 | |
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1066 | #FIXME (Peter Row): Should this be in mesh? |
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1067 | if fid.smoothing != 'Yes': |
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1068 | nodes = nodes.tolist() |
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1069 | triangles = triangles.tolist() |
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1070 | nodes, triangles, boundary = weed(nodes, triangles, boundary) |
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1071 | |
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1072 | try: |
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1073 | mesh = Mesh(nodes, triangles, boundary, geo_reference=geo_reference) |
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1074 | except AssertionError, e: |
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1075 | fid.close() |
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1076 | msg = 'Domain could not be created: %s. "' % e |
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1077 | raise DataDomainError, msg |
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1078 | |
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1079 | quantities = {} |
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1080 | quantities['elevation'] = elevation |
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1081 | quantities['stage'] = stage |
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1082 | quantities['xmomentum'] = xmomentum |
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1083 | quantities['ymomentum'] = ymomentum |
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1084 | |
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1085 | fid.close() |
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1086 | |
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1087 | return mesh, quantities, time |
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1088 | |
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1089 | |
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1090 | def get_time_interp(time, t=None): |
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1091 | """Finds the ratio and index for time interpolation. |
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1092 | time is an array of time steps |
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1093 | t is the sample time. |
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1094 | returns a tuple containing index into time, and ratio |
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1095 | """ |
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1096 | if t is None: |
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1097 | t=time[-1] |
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1098 | index = -1 |
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1099 | ratio = 0. |
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1100 | else: |
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1101 | T = time |
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1102 | tau = t |
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1103 | index=0 |
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1104 | msg = 'Time interval derived from file %s [%s:%s]' \ |
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1105 | % ('FIXMEfilename', T[0], T[-1]) |
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1106 | msg += ' does not match model time: %s' % tau |
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1107 | if tau < time[0]: raise DataTimeError, msg |
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1108 | if tau > time[-1]: raise DataTimeError, msg |
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1109 | while tau > time[index]: index += 1 |
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1110 | while tau < time[index]: index -= 1 |
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1111 | if tau == time[index]: |
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1112 | #Protect against case where tau == time[-1] (last time) |
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1113 | # - also works in general when tau == time[i] |
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1114 | ratio = 0 |
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1115 | else: |
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1116 | #t is now between index and index+1 |
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1117 | ratio = (tau - time[index])/(time[index+1] - time[index]) |
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1118 | |
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1119 | return (index, ratio) |
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1120 | |
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1121 | |
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1122 | |
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1123 | ## |
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1124 | # @brief Interpolate a quantity wrt time. |
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1125 | # @param saved_quantity The quantity to interpolate. |
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1126 | # @param time_interp (index, ratio) |
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1127 | # @return A vector of interpolated values. |
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1128 | def interpolated_quantity(saved_quantity, time_interp): |
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1129 | '''Given an index and ratio, interpolate quantity with respect to time.''' |
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1130 | |
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1131 | index, ratio = time_interp |
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1132 | |
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1133 | Q = saved_quantity |
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1134 | |
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1135 | if ratio > 0: |
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1136 | q = (1-ratio)*Q[index] + ratio*Q[index+1] |
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1137 | else: |
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1138 | q = Q[index] |
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1139 | |
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1140 | #Return vector of interpolated values |
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1141 | return q |
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1142 | |
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1143 | |
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1144 | def weed(coordinates, volumes, boundary=None): |
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1145 | """ Excise all duplicate points. |
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1146 | """ |
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1147 | if isinstance(coordinates, num.ndarray): |
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1148 | coordinates = coordinates.tolist() |
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1149 | if isinstance(volumes, num.ndarray): |
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1150 | volumes = volumes.tolist() |
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1151 | |
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1152 | unique = False |
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1153 | point_dict = {} |
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1154 | same_point = {} |
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1155 | for i in range(len(coordinates)): |
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1156 | point = tuple(coordinates[i]) |
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1157 | if point_dict.has_key(point): |
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1158 | unique = True |
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1159 | same_point[i] = point |
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1160 | #to change all point i references to point j |
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1161 | else: |
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1162 | point_dict[point] = i |
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1163 | same_point[i] = point |
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1164 | |
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1165 | coordinates = [] |
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1166 | i = 0 |
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1167 | for point in point_dict.keys(): |
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1168 | point = tuple(point) |
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1169 | coordinates.append(list(point)) |
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1170 | point_dict[point] = i |
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1171 | i += 1 |
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1172 | |
---|
1173 | for volume in volumes: |
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1174 | for i in range(len(volume)): |
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1175 | index = volume[i] |
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1176 | if index > -1: |
---|
1177 | volume[i] = point_dict[same_point[index]] |
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1178 | |
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1179 | new_boundary = {} |
---|
1180 | if not boundary is None: |
---|
1181 | for segment in boundary.keys(): |
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1182 | point0 = point_dict[same_point[segment[0]]] |
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1183 | point1 = point_dict[same_point[segment[1]]] |
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1184 | label = boundary[segment] |
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1185 | #FIXME should the bounday attributes be concaterated |
---|
1186 | #('exterior, pond') or replaced ('pond')(peter row) |
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1187 | |
---|
1188 | if new_boundary.has_key((point0, point1)): |
---|
1189 | new_boundary[(point0,point1)] = new_boundary[(point0, point1)] |
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1190 | |
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1191 | elif new_boundary.has_key((point1, point0)): |
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1192 | new_boundary[(point1,point0)] = new_boundary[(point1, point0)] |
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1193 | else: new_boundary[(point0, point1)] = label |
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1194 | |
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1195 | boundary = new_boundary |
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1196 | |
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1197 | return coordinates, volumes, boundary |
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1198 | |
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1199 | |
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1200 | |
---|