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 | from Scientific.IO.NetCDF import NetCDFFile |
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10 | |
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11 | from anuga.coordinate_transforms.geo_reference import \ |
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12 | ensure_geo_reference |
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13 | |
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14 | from file_utils import create_filename |
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15 | import numpy as num |
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16 | |
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17 | ## |
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18 | # @brief Generic class for storing output to e.g. visualisation or checkpointing |
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19 | class Data_format: |
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20 | """Generic interface to data formats |
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21 | """ |
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22 | |
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23 | ## |
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24 | # @brief Instantiate this instance. |
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25 | # @param domain |
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26 | # @param extension |
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27 | # @param mode The mode of the underlying file. |
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28 | def __init__(self, domain, extension, mode=netcdf_mode_w): |
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29 | assert mode[0] in ['r', 'w', 'a'], \ |
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30 | "Mode %s must be either:\n" % mode + \ |
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31 | " 'w' (write)\n" + \ |
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32 | " 'r' (read)\n" + \ |
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33 | " 'a' (append)" |
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34 | |
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35 | #Create filename |
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36 | self.filename = create_filename(domain.get_datadir(), |
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37 | domain.get_name(), extension) |
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38 | |
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39 | self.timestep = 0 |
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40 | self.domain = domain |
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41 | |
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42 | # Exclude ghosts in case this is a parallel domain |
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43 | self.number_of_nodes = domain.number_of_full_nodes |
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44 | self.number_of_volumes = domain.number_of_full_triangles |
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45 | #self.number_of_volumes = len(domain) |
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46 | |
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47 | #FIXME: Should we have a general set_precision function? |
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48 | |
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49 | |
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50 | ## |
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51 | # @brief Class for handling checkpoints data |
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52 | # @note This is not operational at the moment |
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53 | class CPT_file(Data_format): |
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54 | """Interface to native NetCDF format (.cpt) to be |
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55 | used for checkpointing (one day) |
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56 | """ |
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57 | |
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58 | ## |
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59 | # @brief Initialize this instantiation. |
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60 | # @param domain ?? |
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61 | # @param mode Mode of underlying data file (default WRITE). |
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62 | def __init__(self, domain, mode=netcdf_mode_w): |
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63 | from Scientific.IO.NetCDF import NetCDFFile |
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64 | |
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65 | self.precision = netcdf_float #Use full precision |
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66 | |
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67 | Data_format.__init__(self, domain, 'sww', mode) |
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68 | |
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69 | # NetCDF file definition |
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70 | fid = NetCDFFile(self.filename, mode) |
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71 | if mode[0] == 'w': |
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72 | # Create new file |
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73 | fid.institution = 'Geoscience Australia' |
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74 | fid.description = 'Checkpoint data' |
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75 | #fid.smooth = domain.smooth |
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76 | fid.order = domain.default_order |
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77 | |
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78 | # Dimension definitions |
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79 | fid.createDimension('number_of_volumes', self.number_of_volumes) |
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80 | fid.createDimension('number_of_vertices', 3) |
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81 | |
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82 | # Store info at all vertices (no smoothing) |
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83 | fid.createDimension('number_of_points', 3*self.number_of_volumes) |
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84 | fid.createDimension('number_of_timesteps', None) #extensible |
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85 | |
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86 | # Variable definitions |
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87 | |
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88 | # Mesh |
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89 | fid.createVariable('x', self.precision, ('number_of_points',)) |
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90 | fid.createVariable('y', self.precision, ('number_of_points',)) |
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91 | |
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92 | |
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93 | fid.createVariable('volumes', netcdf_int, ('number_of_volumes', |
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94 | 'number_of_vertices')) |
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95 | |
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96 | fid.createVariable('time', self.precision, ('number_of_timesteps',)) |
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97 | |
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98 | #Allocate space for all quantities |
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99 | for name in domain.quantities.keys(): |
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100 | fid.createVariable(name, self.precision, |
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101 | ('number_of_timesteps', |
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102 | 'number_of_points')) |
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103 | |
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104 | fid.close() |
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105 | |
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106 | ## |
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107 | # @brief Store connectivity data to underlying data file. |
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108 | def store_checkpoint(self): |
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109 | """Write x,y coordinates of triangles. |
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110 | Write connectivity ( |
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111 | constituting |
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112 | the bed elevation. |
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113 | """ |
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114 | |
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115 | from Scientific.IO.NetCDF import NetCDFFile |
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116 | |
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117 | domain = self.domain |
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118 | |
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119 | #Get NetCDF |
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120 | fid = NetCDFFile(self.filename, netcdf_mode_a) |
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121 | |
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122 | # Get the variables |
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123 | x = fid.variables['x'] |
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124 | y = fid.variables['y'] |
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125 | |
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126 | volumes = fid.variables['volumes'] |
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127 | |
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128 | # Get X, Y and bed elevation Z |
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129 | Q = domain.quantities['elevation'] |
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130 | X,Y,Z,V = Q.get_vertex_values(xy=True, precision=self.precision) |
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131 | |
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132 | x[:] = X.astype(self.precision) |
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133 | y[:] = Y.astype(self.precision) |
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134 | z[:] = Z.astype(self.precision) |
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135 | |
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136 | volumes[:] = V |
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137 | |
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138 | fid.close() |
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139 | |
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140 | ## |
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141 | # @brief Store time and named quantities to underlying data file. |
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142 | # @param name |
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143 | def store_timestep(self, name): |
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144 | """Store time and named quantity to file |
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145 | """ |
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146 | |
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147 | from Scientific.IO.NetCDF import NetCDFFile |
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148 | from time import sleep |
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149 | |
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150 | #Get NetCDF |
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151 | retries = 0 |
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152 | file_open = False |
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153 | while not file_open and retries < 10: |
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154 | try: |
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155 | fid = NetCDFFile(self.filename, netcdf_mode_a) |
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156 | except IOError: |
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157 | #This could happen if someone was reading the file. |
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158 | #In that case, wait a while and try again |
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159 | msg = 'Warning (store_timestep): File %s could not be opened' \ |
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160 | ' - trying again' % self.filename |
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161 | log.critical(msg) |
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162 | retries += 1 |
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163 | sleep(1) |
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164 | else: |
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165 | file_open = True |
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166 | |
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167 | if not file_open: |
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168 | msg = 'File %s could not be opened for append' % self.filename |
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169 | raise DataFileNotOpenError, msg |
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170 | |
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171 | domain = self.domain |
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172 | |
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173 | # Get the variables |
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174 | time = fid.variables['time'] |
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175 | stage = fid.variables['stage'] |
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176 | i = len(time) |
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177 | |
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178 | #Store stage |
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179 | time[i] = self.domain.time |
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180 | |
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181 | # Get quantity |
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182 | Q = domain.quantities[name] |
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183 | A,V = Q.get_vertex_values(xy=False, precision=self.precision) |
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184 | |
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185 | stage[i,:] = A.astype(self.precision) |
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186 | |
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187 | #Flush and close |
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188 | fid.sync() |
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189 | fid.close() |
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190 | |
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191 | |
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192 | class SWW_file(Data_format): |
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193 | """Interface to native NetCDF format (.sww) for storing model output |
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194 | |
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195 | There are two kinds of data |
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196 | |
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197 | 1: Constant data: Vertex coordinates and field values. Stored once |
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198 | 2: Variable data: Conserved quantities. Stored once per timestep. |
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199 | |
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200 | All data is assumed to reside at vertex locations. |
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201 | """ |
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202 | |
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203 | ## |
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204 | # @brief Instantiate this instance. |
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205 | # @param domain ?? |
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206 | # @param mode Mode of the underlying data file. |
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207 | # @param max_size ?? |
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208 | # @param recursion ?? |
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209 | # @note Prepare the underlying data file if mode starts with 'w'. |
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210 | def __init__(self, domain, |
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211 | mode=netcdf_mode_w, max_size=2000000000, recursion=False): |
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212 | from Scientific.IO.NetCDF import NetCDFFile |
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213 | |
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214 | self.precision = netcdf_float32 # Use single precision for quantities |
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215 | self.recursion = recursion |
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216 | self.mode = mode |
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217 | if hasattr(domain, 'max_size'): |
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218 | self.max_size = domain.max_size # File size max is 2Gig |
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219 | else: |
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220 | self.max_size = max_size |
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221 | if hasattr(domain, 'minimum_storable_height'): |
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222 | self.minimum_storable_height = domain.minimum_storable_height |
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223 | else: |
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224 | self.minimum_storable_height = default_minimum_storable_height |
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225 | |
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226 | # Call parent constructor |
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227 | Data_format.__init__(self, domain, 'sww', mode) |
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228 | |
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229 | # Get static and dynamic quantities from domain |
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230 | static_quantities = [] |
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231 | dynamic_quantities = [] |
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232 | |
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233 | for q in domain.quantities_to_be_stored: |
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234 | flag = domain.quantities_to_be_stored[q] |
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235 | |
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236 | msg = 'Quantity %s is requested to be stored ' % q |
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237 | msg += 'but it does not exist in domain.quantities' |
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238 | assert q in domain.quantities, msg |
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239 | |
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240 | assert flag in [1,2] |
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241 | if flag == 1: static_quantities.append(q) |
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242 | if flag == 2: dynamic_quantities.append(q) |
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243 | |
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244 | |
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245 | # NetCDF file definition |
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246 | fid = NetCDFFile(self.filename, mode) |
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247 | if mode[0] == 'w': |
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248 | description = 'Output from anuga.abstract_2d_finite_volumes ' \ |
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249 | 'suitable for plotting' |
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250 | |
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251 | self.writer = Write_sww(static_quantities, dynamic_quantities) |
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252 | self.writer.store_header(fid, |
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253 | domain.starttime, |
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254 | self.number_of_volumes, |
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255 | self.domain.number_of_full_nodes, |
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256 | description=description, |
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257 | smoothing=domain.smooth, |
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258 | order=domain.default_order, |
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259 | sww_precision=self.precision) |
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260 | |
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261 | # Extra optional information |
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262 | if hasattr(domain, 'texture'): |
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263 | fid.texture = domain.texture |
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264 | |
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265 | if domain.quantities_to_be_monitored is not None: |
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266 | fid.createDimension('singleton', 1) |
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267 | fid.createDimension('two', 2) |
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268 | |
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269 | poly = domain.monitor_polygon |
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270 | if poly is not None: |
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271 | N = len(poly) |
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272 | fid.createDimension('polygon_length', N) |
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273 | fid.createVariable('extrema.polygon', |
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274 | self.precision, |
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275 | ('polygon_length', 'two')) |
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276 | fid.variables['extrema.polygon'][:] = poly |
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277 | |
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278 | interval = domain.monitor_time_interval |
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279 | if interval is not None: |
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280 | fid.createVariable('extrema.time_interval', |
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281 | self.precision, |
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282 | ('two',)) |
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283 | fid.variables['extrema.time_interval'][:] = interval |
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284 | |
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285 | for q in domain.quantities_to_be_monitored: |
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286 | fid.createVariable(q + '.extrema', self.precision, |
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287 | ('numbers_in_range',)) |
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288 | fid.createVariable(q + '.min_location', self.precision, |
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289 | ('numbers_in_range',)) |
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290 | fid.createVariable(q + '.max_location', self.precision, |
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291 | ('numbers_in_range',)) |
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292 | fid.createVariable(q + '.min_time', self.precision, |
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293 | ('singleton',)) |
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294 | fid.createVariable(q + '.max_time', self.precision, |
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295 | ('singleton',)) |
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296 | |
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297 | fid.close() |
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298 | |
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299 | ## |
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300 | # @brief Store connectivity data into the underlying data file. |
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301 | def store_connectivity(self): |
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302 | """Store information about nodes, triangles and static quantities |
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303 | |
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304 | Writes x,y coordinates of triangles and their connectivity. |
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305 | |
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306 | Store also any quantity that has been identified as static. |
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307 | """ |
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308 | |
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309 | # FIXME: Change name to reflect the fact thta this function |
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310 | # stores both connectivity (triangulation) and static quantities |
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311 | |
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312 | from Scientific.IO.NetCDF import NetCDFFile |
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313 | |
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314 | domain = self.domain |
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315 | |
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316 | # append to the NetCDF file |
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317 | fid = NetCDFFile(self.filename, netcdf_mode_a) |
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318 | |
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319 | # Get X, Y from one (any) of the quantities |
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320 | Q = domain.quantities.values()[0] |
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321 | X,Y,_,V = Q.get_vertex_values(xy=True, precision=self.precision) |
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322 | |
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323 | # store the connectivity data |
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324 | points = num.concatenate((X[:,num.newaxis],Y[:,num.newaxis]), axis=1) |
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325 | self.writer.store_triangulation(fid, |
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326 | points, |
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327 | V.astype(num.float32), |
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328 | points_georeference=\ |
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329 | domain.geo_reference) |
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330 | |
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331 | |
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332 | # Get names of static quantities |
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333 | static_quantities = {} |
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334 | for name in self.writer.static_quantities: |
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335 | Q = domain.quantities[name] |
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336 | A, _ = Q.get_vertex_values(xy=False, |
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337 | precision=self.precision) |
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338 | static_quantities[name] = A |
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339 | |
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340 | # Store static quantities |
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341 | self.writer.store_static_quantities(fid, **static_quantities) |
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342 | |
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343 | fid.close() |
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344 | |
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345 | ## |
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346 | # @brief Store time and time dependent quantities |
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347 | # to the underlying data file. |
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348 | def store_timestep(self): |
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349 | """Store time and time dependent quantities |
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350 | """ |
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351 | |
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352 | from Scientific.IO.NetCDF import NetCDFFile |
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353 | import types |
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354 | from time import sleep |
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355 | from os import stat |
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356 | |
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357 | # Get NetCDF |
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358 | retries = 0 |
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359 | file_open = False |
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360 | while not file_open and retries < 10: |
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361 | try: |
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362 | # Open existing file |
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363 | fid = NetCDFFile(self.filename, netcdf_mode_a) |
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364 | except IOError: |
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365 | # This could happen if someone was reading the file. |
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366 | # In that case, wait a while and try again |
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367 | msg = 'Warning (store_timestep): File %s could not be opened' \ |
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368 | % self.filename |
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369 | msg += ' - trying step %s again' % self.domain.time |
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370 | log.critical(msg) |
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371 | retries += 1 |
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372 | sleep(1) |
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373 | else: |
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374 | file_open = True |
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375 | |
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376 | if not file_open: |
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377 | msg = 'File %s could not be opened for append' % self.filename |
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378 | raise DataFileNotOpenError, msg |
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379 | |
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380 | # Check to see if the file is already too big: |
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381 | time = fid.variables['time'] |
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382 | i = len(time) + 1 |
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383 | file_size = stat(self.filename)[6] |
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384 | file_size_increase = file_size / i |
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385 | if file_size + file_size_increase > self.max_size * 2**self.recursion: |
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386 | # In order to get the file name and start time correct, |
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387 | # I change the domain.filename and domain.starttime. |
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388 | # This is the only way to do this without changing |
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389 | # other modules (I think). |
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390 | |
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391 | # Write a filename addon that won't break the anuga viewers |
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392 | # (10.sww is bad) |
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393 | filename_ext = '_time_%s' % self.domain.time |
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394 | filename_ext = filename_ext.replace('.', '_') |
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395 | |
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396 | # Remember the old filename, then give domain a |
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397 | # name with the extension |
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398 | old_domain_filename = self.domain.get_name() |
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399 | if not self.recursion: |
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400 | self.domain.set_name(old_domain_filename + filename_ext) |
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401 | |
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402 | # Temporarily change the domain starttime to the current time |
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403 | old_domain_starttime = self.domain.starttime |
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404 | self.domain.starttime = self.domain.get_time() |
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405 | |
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406 | # Build a new data_structure. |
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407 | next_data_structure = SWW_file(self.domain, mode=self.mode, |
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408 | max_size=self.max_size, |
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409 | recursion=self.recursion+1) |
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410 | if not self.recursion: |
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411 | log.critical(' file_size = %s' % file_size) |
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412 | log.critical(' saving file to %s' |
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413 | % next_data_structure.filename) |
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414 | |
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415 | # Set up the new data_structure |
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416 | self.domain.writer = next_data_structure |
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417 | |
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418 | # Store connectivity and first timestep |
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419 | next_data_structure.store_connectivity() |
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420 | next_data_structure.store_timestep() |
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421 | fid.sync() |
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422 | fid.close() |
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423 | |
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424 | # Restore the old starttime and filename |
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425 | self.domain.starttime = old_domain_starttime |
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426 | self.domain.set_name(old_domain_filename) |
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427 | else: |
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428 | self.recursion = False |
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429 | domain = self.domain |
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430 | |
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431 | # Get the variables |
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432 | time = fid.variables['time'] |
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433 | i = len(time) |
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434 | |
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435 | if 'stage' in self.writer.dynamic_quantities: |
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436 | # Select only those values for stage, |
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437 | # xmomentum and ymomentum (if stored) where |
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438 | # depth exceeds minimum_storable_height |
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439 | # |
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440 | # In this branch it is assumed that elevation |
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441 | # is also available as a quantity |
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442 | |
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443 | Q = domain.quantities['stage'] |
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444 | w, _ = Q.get_vertex_values(xy=False) |
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445 | |
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446 | Q = domain.quantities['elevation'] |
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447 | z, _ = Q.get_vertex_values(xy=False) |
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448 | |
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449 | storable_indices = (w-z >= self.minimum_storable_height) |
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450 | else: |
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451 | # Very unlikely branch |
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452 | storable_indices = None # This means take all |
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453 | |
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454 | |
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455 | # Now store dynamic quantities |
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456 | dynamic_quantities = {} |
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457 | for name in self.writer.dynamic_quantities: |
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458 | netcdf_array = fid.variables[name] |
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459 | |
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460 | Q = domain.quantities[name] |
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461 | A, _ = Q.get_vertex_values(xy=False, |
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462 | precision=self.precision) |
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463 | |
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464 | if storable_indices is not None: |
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465 | if name == 'stage': |
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466 | A = num.choose(storable_indices, (z, A)) |
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467 | |
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468 | if name in ['xmomentum', 'ymomentum']: |
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469 | # Get xmomentum where depth exceeds |
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470 | # minimum_storable_height |
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471 | |
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472 | # Define a zero vector of same size and type as A |
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473 | # for use with momenta |
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474 | null = num.zeros(num.size(A), A.dtype.char) |
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475 | A = num.choose(storable_indices, (null, A)) |
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476 | |
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477 | dynamic_quantities[name] = A |
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478 | |
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479 | |
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480 | # Store dynamic quantities |
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481 | self.writer.store_quantities(fid, |
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482 | time=self.domain.time, |
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483 | sww_precision=self.precision, |
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484 | **dynamic_quantities) |
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485 | |
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486 | |
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487 | # Update extrema if requested |
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488 | domain = self.domain |
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489 | if domain.quantities_to_be_monitored is not None: |
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490 | for q, info in domain.quantities_to_be_monitored.items(): |
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491 | if info['min'] is not None: |
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492 | fid.variables[q + '.extrema'][0] = info['min'] |
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493 | fid.variables[q + '.min_location'][:] = \ |
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494 | info['min_location'] |
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495 | fid.variables[q + '.min_time'][0] = info['min_time'] |
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496 | |
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497 | if info['max'] is not None: |
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498 | fid.variables[q + '.extrema'][1] = info['max'] |
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499 | fid.variables[q + '.max_location'][:] = \ |
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500 | info['max_location'] |
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501 | fid.variables[q + '.max_time'][0] = info['max_time'] |
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502 | |
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503 | # Flush and close |
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504 | fid.sync() |
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505 | fid.close() |
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506 | |
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507 | |
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508 | ## |
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509 | # @brief Class to open an sww file so that domain can be populated with quantity values |
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510 | class Read_sww: |
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511 | |
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512 | def __init__(self, source): |
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513 | """The source parameter is assumed to be a NetCDF sww file. |
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514 | """ |
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515 | |
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516 | self.source = source |
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517 | |
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518 | self.frame_number = 0 |
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519 | |
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520 | fin = NetCDFFile(self.source, 'r') |
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521 | |
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522 | self.time = num.array(fin.variables['time'], num.float) |
---|
523 | self.last_frame_number = self.time.shape[0] - 1 |
---|
524 | |
---|
525 | self.frames = num.arange(self.last_frame_number+1) |
---|
526 | |
---|
527 | fin.close() |
---|
528 | |
---|
529 | self.read_mesh() |
---|
530 | |
---|
531 | self.quantities = {} |
---|
532 | |
---|
533 | self.read_quantities() |
---|
534 | |
---|
535 | |
---|
536 | def read_mesh(self): |
---|
537 | fin = NetCDFFile(self.source, 'r') |
---|
538 | |
---|
539 | self.vertices = num.array(fin.variables['volumes'], num.int) |
---|
540 | |
---|
541 | self.x = x = num.array(fin.variables['x'], num.float) |
---|
542 | self.y = y = num.array(fin.variables['y'], num.float) |
---|
543 | |
---|
544 | assert len(self.x) == len(self.y) |
---|
545 | |
---|
546 | self.xmin = num.min(x) |
---|
547 | self.xmax = num.max(x) |
---|
548 | self.ymin = num.min(y) |
---|
549 | self.ymax = num.max(y) |
---|
550 | |
---|
551 | |
---|
552 | |
---|
553 | fin.close() |
---|
554 | |
---|
555 | def read_quantities(self, frame_number=0): |
---|
556 | |
---|
557 | assert frame_number >= 0 and frame_number <= self.last_frame_number |
---|
558 | |
---|
559 | self.frame_number = frame_number |
---|
560 | |
---|
561 | M = len(self.x)/3 |
---|
562 | |
---|
563 | fin = NetCDFFile(self.source, 'r') |
---|
564 | |
---|
565 | for q in filter(lambda n:n != 'x' and n != 'y' and n != 'time' and n != 'volumes' and \ |
---|
566 | '_range' not in n, \ |
---|
567 | fin.variables.keys()): |
---|
568 | if len(fin.variables[q].shape) == 1: # Not a time-varying quantity |
---|
569 | self.quantities[q] = num.ravel(num.array(fin.variables[q], num.float)).reshape(M,3) |
---|
570 | else: # Time-varying, get the current timestep data |
---|
571 | self.quantities[q] = num.array(fin.variables[q][self.frame_number], num.float).reshape(M,3) |
---|
572 | fin.close() |
---|
573 | return self.quantities |
---|
574 | |
---|
575 | def get_bounds(self): |
---|
576 | return [self.xmin, self.xmax, self.ymin, self.ymax] |
---|
577 | |
---|
578 | def get_last_frame_number(self): |
---|
579 | return self.last_frame_number |
---|
580 | |
---|
581 | def get_time(self): |
---|
582 | return self.time[self.frame_number] |
---|
583 | |
---|
584 | |
---|
585 | # @brief A class to write an SWW file. |
---|
586 | class Write_sww: |
---|
587 | from anuga.shallow_water.shallow_water_domain import Domain |
---|
588 | |
---|
589 | RANGE = '_range' |
---|
590 | EXTREMA = ':extrema' |
---|
591 | |
---|
592 | ## |
---|
593 | # brief Instantiate the SWW writer class. |
---|
594 | def __init__(self, static_quantities, dynamic_quantities): |
---|
595 | """Initialise Write_sww with two list af quantity names: |
---|
596 | |
---|
597 | static_quantities (e.g. elevation or friction): |
---|
598 | Stored once at the beginning of the simulation in a 1D array |
---|
599 | of length number_of_points |
---|
600 | dynamic_quantities (e.g stage): |
---|
601 | Stored every timestep in a 2D array with |
---|
602 | dimensions number_of_points X number_of_timesteps |
---|
603 | |
---|
604 | """ |
---|
605 | self.static_quantities = static_quantities |
---|
606 | self.dynamic_quantities = dynamic_quantities |
---|
607 | |
---|
608 | |
---|
609 | ## |
---|
610 | # @brief Store a header in the SWW file. |
---|
611 | # @param outfile Open handle to the file that will be written. |
---|
612 | # @param times A list of time slices *or* a start time. |
---|
613 | # @param number_of_volumes The number of triangles. |
---|
614 | # @param number_of_points The number of points. |
---|
615 | # @param description The internal file description string. |
---|
616 | # @param smoothing True if smoothing is to be used. |
---|
617 | # @param order |
---|
618 | # @param sww_precision Data type of the quantity written (netcdf constant) |
---|
619 | # @param verbose True if this function is to be verbose. |
---|
620 | # @note If 'times' is a list, the info will be made relative. |
---|
621 | def store_header(self, |
---|
622 | outfile, |
---|
623 | times, |
---|
624 | number_of_volumes, |
---|
625 | number_of_points, |
---|
626 | description='Generated by ANUGA', |
---|
627 | smoothing=True, |
---|
628 | order=1, |
---|
629 | sww_precision=netcdf_float32, |
---|
630 | verbose=False): |
---|
631 | """Write an SWW file header. |
---|
632 | |
---|
633 | outfile - the open file that will be written |
---|
634 | times - A list of the time slice times OR a start time |
---|
635 | Note, if a list is given the info will be made relative. |
---|
636 | number_of_volumes - the number of triangles |
---|
637 | """ |
---|
638 | |
---|
639 | outfile.institution = 'Geoscience Australia' |
---|
640 | outfile.description = description |
---|
641 | |
---|
642 | # For sww compatibility |
---|
643 | if smoothing is True: |
---|
644 | # Smoothing to be depreciated |
---|
645 | outfile.smoothing = 'Yes' |
---|
646 | outfile.vertices_are_stored_uniquely = 'False' |
---|
647 | else: |
---|
648 | # Smoothing to be depreciated |
---|
649 | outfile.smoothing = 'No' |
---|
650 | outfile.vertices_are_stored_uniquely = 'True' |
---|
651 | outfile.order = order |
---|
652 | |
---|
653 | try: |
---|
654 | revision_number = get_revision_number() |
---|
655 | except: |
---|
656 | revision_number = None |
---|
657 | # Allow None to be stored as a string |
---|
658 | outfile.revision_number = str(revision_number) |
---|
659 | |
---|
660 | # This is being used to seperate one number from a list. |
---|
661 | # what it is actually doing is sorting lists from numeric arrays. |
---|
662 | if isinstance(times, (list, num.ndarray)): |
---|
663 | number_of_times = len(times) |
---|
664 | times = ensure_numeric(times) |
---|
665 | if number_of_times == 0: |
---|
666 | starttime = 0 |
---|
667 | else: |
---|
668 | starttime = times[0] |
---|
669 | times = times - starttime #Store relative times |
---|
670 | else: |
---|
671 | number_of_times = 0 |
---|
672 | starttime = times |
---|
673 | |
---|
674 | |
---|
675 | outfile.starttime = starttime |
---|
676 | |
---|
677 | # dimension definitions |
---|
678 | outfile.createDimension('number_of_volumes', number_of_volumes) |
---|
679 | outfile.createDimension('number_of_vertices', 3) |
---|
680 | outfile.createDimension('numbers_in_range', 2) |
---|
681 | |
---|
682 | if smoothing is True: |
---|
683 | outfile.createDimension('number_of_points', number_of_points) |
---|
684 | # FIXME(Ole): This will cause sww files for parallel domains to |
---|
685 | # have ghost nodes stored (but not used by triangles). |
---|
686 | # To clean this up, we have to change get_vertex_values and |
---|
687 | # friends in quantity.py (but I can't be bothered right now) |
---|
688 | else: |
---|
689 | outfile.createDimension('number_of_points', 3*number_of_volumes) |
---|
690 | |
---|
691 | outfile.createDimension('number_of_timesteps', number_of_times) |
---|
692 | |
---|
693 | # variable definitions |
---|
694 | outfile.createVariable('x', sww_precision, ('number_of_points',)) |
---|
695 | outfile.createVariable('y', sww_precision, ('number_of_points',)) |
---|
696 | |
---|
697 | outfile.createVariable('volumes', netcdf_int, ('number_of_volumes', |
---|
698 | 'number_of_vertices')) |
---|
699 | |
---|
700 | # Doing sww_precision instead of Float gives cast errors. |
---|
701 | outfile.createVariable('time', netcdf_float, |
---|
702 | ('number_of_timesteps',)) |
---|
703 | |
---|
704 | |
---|
705 | for q in self.static_quantities: |
---|
706 | |
---|
707 | outfile.createVariable(q, sww_precision, |
---|
708 | ('number_of_points',)) |
---|
709 | |
---|
710 | outfile.createVariable(q + Write_sww.RANGE, sww_precision, |
---|
711 | ('numbers_in_range',)) |
---|
712 | |
---|
713 | # Initialise ranges with small and large sentinels. |
---|
714 | # If this was in pure Python we could have used None sensibly |
---|
715 | outfile.variables[q+Write_sww.RANGE][0] = max_float # Min |
---|
716 | outfile.variables[q+Write_sww.RANGE][1] = -max_float # Max |
---|
717 | |
---|
718 | #if 'elevation' in self.static_quantities: |
---|
719 | # # FIXME: Backwards compat - get rid of z once old view has retired |
---|
720 | # outfile.createVariable('z', sww_precision, |
---|
721 | # ('number_of_points',)) |
---|
722 | |
---|
723 | for q in self.dynamic_quantities: |
---|
724 | outfile.createVariable(q, sww_precision, ('number_of_timesteps', |
---|
725 | 'number_of_points')) |
---|
726 | outfile.createVariable(q + Write_sww.RANGE, sww_precision, |
---|
727 | ('numbers_in_range',)) |
---|
728 | |
---|
729 | # Initialise ranges with small and large sentinels. |
---|
730 | # If this was in pure Python we could have used None sensibly |
---|
731 | outfile.variables[q+Write_sww.RANGE][0] = max_float # Min |
---|
732 | outfile.variables[q+Write_sww.RANGE][1] = -max_float # Max |
---|
733 | |
---|
734 | if isinstance(times, (list, num.ndarray)): |
---|
735 | outfile.variables['time'][:] = times # Store time relative |
---|
736 | |
---|
737 | if verbose: |
---|
738 | log.critical('------------------------------------------------') |
---|
739 | log.critical('Statistics:') |
---|
740 | log.critical(' t in [%f, %f], len(t) == %d' |
---|
741 | % (num.min(times), num.max(times), len(times.flat))) |
---|
742 | |
---|
743 | ## |
---|
744 | # @brief Store triangulation data in the underlying file. |
---|
745 | # @param outfile Open handle to underlying file. |
---|
746 | # @param points_utm List or array of points in UTM. |
---|
747 | # @param volumes |
---|
748 | # @param zone |
---|
749 | # @param new_origin georeference that the points can be set to. |
---|
750 | # @param points_georeference The georeference of the points_utm. |
---|
751 | # @param verbose True if this function is to be verbose. |
---|
752 | def store_triangulation(self, |
---|
753 | outfile, |
---|
754 | points_utm, |
---|
755 | volumes, |
---|
756 | zone=None, |
---|
757 | new_origin=None, |
---|
758 | points_georeference=None, |
---|
759 | verbose=False): |
---|
760 | """ |
---|
761 | new_origin - qa georeference that the points can be set to. (Maybe |
---|
762 | do this before calling this function.) |
---|
763 | |
---|
764 | points_utm - currently a list or array of the points in UTM. |
---|
765 | points_georeference - the georeference of the points_utm |
---|
766 | |
---|
767 | How about passing new_origin and current_origin. |
---|
768 | If you get both, do a convertion from the old to the new. |
---|
769 | |
---|
770 | If you only get new_origin, the points are absolute, |
---|
771 | convert to relative |
---|
772 | |
---|
773 | if you only get the current_origin the points are relative, store |
---|
774 | as relative. |
---|
775 | |
---|
776 | if you get no georefs create a new georef based on the minimums of |
---|
777 | points_utm. (Another option would be to default to absolute) |
---|
778 | |
---|
779 | Yes, and this is done in another part of the code. |
---|
780 | Probably geospatial. |
---|
781 | |
---|
782 | If you don't supply either geo_refs, then supply a zone. If not |
---|
783 | the default zone will be used. |
---|
784 | |
---|
785 | precon: |
---|
786 | header has been called. |
---|
787 | """ |
---|
788 | |
---|
789 | number_of_points = len(points_utm) |
---|
790 | volumes = num.array(volumes) |
---|
791 | points_utm = num.array(points_utm) |
---|
792 | |
---|
793 | # Given the two geo_refs and the points, do the stuff |
---|
794 | # described in the method header |
---|
795 | # if this is needed else where, pull out as a function |
---|
796 | points_georeference = ensure_geo_reference(points_georeference) |
---|
797 | new_origin = ensure_geo_reference(new_origin) |
---|
798 | if new_origin is None and points_georeference is not None: |
---|
799 | points = points_utm |
---|
800 | geo_ref = points_georeference |
---|
801 | else: |
---|
802 | if new_origin is None: |
---|
803 | new_origin = Geo_reference(zone, min(points_utm[:,0]), |
---|
804 | min(points_utm[:,1])) |
---|
805 | points = new_origin.change_points_geo_ref(points_utm, |
---|
806 | points_georeference) |
---|
807 | geo_ref = new_origin |
---|
808 | |
---|
809 | # At this stage I need a georef and points |
---|
810 | # the points are relative to the georef |
---|
811 | geo_ref.write_NetCDF(outfile) |
---|
812 | |
---|
813 | # This will put the geo ref in the middle |
---|
814 | #geo_ref = Geo_reference(refzone,(max(x)+min(x))/2.0,(max(x)+min(y))/2.) |
---|
815 | |
---|
816 | x = points[:,0] |
---|
817 | y = points[:,1] |
---|
818 | |
---|
819 | if verbose: |
---|
820 | log.critical('------------------------------------------------') |
---|
821 | log.critical('More Statistics:') |
---|
822 | log.critical(' Extent (/lon):') |
---|
823 | log.critical(' x in [%f, %f], len(lat) == %d' |
---|
824 | % (min(x), max(x), len(x))) |
---|
825 | log.critical(' y in [%f, %f], len(lon) == %d' |
---|
826 | % (min(y), max(y), len(y))) |
---|
827 | #log.critical(' z in [%f, %f], len(z) == %d' |
---|
828 | # % (min(elevation), max(elevation), len(elevation))) |
---|
829 | log.critical('geo_ref: %s' % str(geo_ref)) |
---|
830 | log.critical('------------------------------------------------') |
---|
831 | |
---|
832 | outfile.variables['x'][:] = points[:,0] #- geo_ref.get_xllcorner() |
---|
833 | outfile.variables['y'][:] = points[:,1] #- geo_ref.get_yllcorner() |
---|
834 | outfile.variables['volumes'][:] = volumes.astype(num.int32) #On Opteron 64 |
---|
835 | |
---|
836 | |
---|
837 | |
---|
838 | # @brief Write the static quantity data to the underlying file. |
---|
839 | # @param outfile Handle to open underlying file. |
---|
840 | # @param sww_precision Format of quantity data to write (default Float32). |
---|
841 | # @param verbose True if this function is to be verbose. |
---|
842 | # @param **quant |
---|
843 | def store_static_quantities(self, |
---|
844 | outfile, |
---|
845 | sww_precision=num.float32, |
---|
846 | verbose=False, |
---|
847 | **quant): |
---|
848 | """ |
---|
849 | Write the static quantity info. |
---|
850 | |
---|
851 | **quant is extra keyword arguments passed in. These must be |
---|
852 | the numpy arrays to be stored in the sww file at each timestep. |
---|
853 | |
---|
854 | The argument sww_precision allows for storing as either |
---|
855 | * single precision (default): num.float32 |
---|
856 | * double precision: num.float64 or num.float |
---|
857 | |
---|
858 | Precondition: |
---|
859 | store_triangulation and |
---|
860 | store_header have been called. |
---|
861 | """ |
---|
862 | |
---|
863 | # The dictionary quant must contain numpy arrays for each name. |
---|
864 | # These will typically be quantities from Domain such as friction |
---|
865 | # |
---|
866 | # Arrays not listed in static_quantitiues will be ignored, silently. |
---|
867 | # |
---|
868 | # This method will also write the ranges for each quantity, |
---|
869 | # e.g. stage_range, xmomentum_range and ymomentum_range |
---|
870 | for q in self.static_quantities: |
---|
871 | if not quant.has_key(q): |
---|
872 | msg = 'Values for quantity %s was not specified in ' % q |
---|
873 | msg += 'store_quantities so they cannot be stored.' |
---|
874 | raise NewQuantity, msg |
---|
875 | else: |
---|
876 | q_values = ensure_numeric(quant[q]) |
---|
877 | |
---|
878 | x = q_values.astype(sww_precision) |
---|
879 | outfile.variables[q][:] = x |
---|
880 | |
---|
881 | # This populates the _range values |
---|
882 | outfile.variables[q + Write_sww.RANGE][0] = num.min(x) |
---|
883 | outfile.variables[q + Write_sww.RANGE][1] = num.max(x) |
---|
884 | |
---|
885 | # FIXME: Hack for backwards compatibility with old viewer |
---|
886 | #if 'elevation' in self.static_quantities: |
---|
887 | # outfile.variables['z'][:] = outfile.variables['elevation'][:] |
---|
888 | |
---|
889 | |
---|
890 | |
---|
891 | |
---|
892 | |
---|
893 | ## |
---|
894 | # @brief Write the quantity data to the underlying file. |
---|
895 | # @param outfile Handle to open underlying file. |
---|
896 | # @param sww_precision Format of quantity data to write (default Float32). |
---|
897 | # @param slice_index |
---|
898 | # @param time |
---|
899 | # @param verbose True if this function is to be verbose. |
---|
900 | # @param **quant |
---|
901 | def store_quantities(self, |
---|
902 | outfile, |
---|
903 | sww_precision=num.float32, |
---|
904 | slice_index=None, |
---|
905 | time=None, |
---|
906 | verbose=False, |
---|
907 | **quant): |
---|
908 | """ |
---|
909 | Write the quantity info at each timestep. |
---|
910 | |
---|
911 | **quant is extra keyword arguments passed in. These must be |
---|
912 | the numpy arrays to be stored in the sww file at each timestep. |
---|
913 | |
---|
914 | if the time array is already been built, use the slice_index |
---|
915 | to specify the index. |
---|
916 | |
---|
917 | Otherwise, use time to increase the time dimension |
---|
918 | |
---|
919 | Maybe make this general, but the viewer assumes these quantities, |
---|
920 | so maybe we don't want it general - unless the viewer is general |
---|
921 | |
---|
922 | The argument sww_precision allows for storing as either |
---|
923 | * single precision (default): num.float32 |
---|
924 | * double precision: num.float64 or num.float |
---|
925 | |
---|
926 | Precondition: |
---|
927 | store_triangulation and |
---|
928 | store_header have been called. |
---|
929 | """ |
---|
930 | |
---|
931 | if time is not None: |
---|
932 | file_time = outfile.variables['time'] |
---|
933 | slice_index = len(file_time) |
---|
934 | file_time[slice_index] = time |
---|
935 | else: |
---|
936 | slice_index = int(slice_index) # Has to be cast in case it was numpy.int |
---|
937 | |
---|
938 | # Write the named dynamic quantities |
---|
939 | # The dictionary quant must contain numpy arrays for each name. |
---|
940 | # These will typically be the conserved quantities from Domain |
---|
941 | # (Typically stage, xmomentum, ymomentum). |
---|
942 | # |
---|
943 | # Arrays not listed in dynamic_quantitiues will be ignored, silently. |
---|
944 | # |
---|
945 | # This method will also write the ranges for each quantity, |
---|
946 | # e.g. stage_range, xmomentum_range and ymomentum_range |
---|
947 | for q in self.dynamic_quantities: |
---|
948 | if not quant.has_key(q): |
---|
949 | msg = 'Values for quantity %s was not specified in ' % q |
---|
950 | msg += 'store_quantities so they cannot be stored.' |
---|
951 | raise NewQuantity, msg |
---|
952 | else: |
---|
953 | q_values = ensure_numeric(quant[q]) |
---|
954 | |
---|
955 | x = q_values.astype(sww_precision) |
---|
956 | outfile.variables[q][slice_index] = x |
---|
957 | |
---|
958 | |
---|
959 | # This updates the _range values |
---|
960 | q_range = outfile.variables[q + Write_sww.RANGE][:] |
---|
961 | q_values_min = num.min(q_values) |
---|
962 | if q_values_min < q_range[0]: |
---|
963 | outfile.variables[q + Write_sww.RANGE][0] = q_values_min |
---|
964 | q_values_max = num.max(q_values) |
---|
965 | if q_values_max > q_range[1]: |
---|
966 | outfile.variables[q + Write_sww.RANGE][1] = q_values_max |
---|
967 | |
---|
968 | ## |
---|
969 | # @brief Print the quantities in the underlying file. |
---|
970 | # @param outfile UNUSED. |
---|
971 | def verbose_quantities(self, outfile): |
---|
972 | log.critical('------------------------------------------------') |
---|
973 | log.critical('More Statistics:') |
---|
974 | for q in self.dynamic_quantities: |
---|
975 | log.critical(' %s in [%f, %f]' |
---|
976 | % (q, outfile.variables[q+Write_sww.RANGE][0], |
---|
977 | outfile.variables[q+Write_sww.RANGE][1])) |
---|
978 | log.critical('------------------------------------------------') |
---|
979 | |
---|