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 anuga.coordinate_transforms.geo_reference import \ |
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13 | ensure_geo_reference |
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14 | |
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15 | from file_utils import create_filename |
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16 | import numpy as num |
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17 | |
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18 | ## |
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19 | # @brief Generic class for storing output to e.g. visualisation or checkpointing |
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20 | class Data_format: |
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21 | """Generic interface to data formats |
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22 | """ |
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23 | |
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24 | ## |
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25 | # @brief Instantiate this instance. |
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26 | # @param domain |
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27 | # @param extension |
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28 | # @param mode The mode of the underlying file. |
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29 | def __init__(self, domain, extension, mode=netcdf_mode_w): |
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30 | assert mode[0] in ['r', 'w', 'a'], \ |
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31 | "Mode %s must be either:\n" % mode + \ |
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32 | " 'w' (write)\n" + \ |
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33 | " 'r' (read)\n" + \ |
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34 | " 'a' (append)" |
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35 | |
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36 | #Create filename |
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37 | self.filename = create_filename(domain.get_datadir(), |
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38 | domain.get_name(), extension) |
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39 | |
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40 | self.timestep = 0 |
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41 | self.domain = domain |
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42 | |
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43 | # Exclude ghosts in case this is a parallel domain |
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44 | self.number_of_nodes = domain.number_of_full_nodes |
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45 | self.number_of_volumes = domain.number_of_full_triangles |
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46 | #self.number_of_volumes = len(domain) |
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47 | |
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48 | #FIXME: Should we have a general set_precision function? |
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49 | |
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50 | |
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51 | ## |
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52 | # @brief Class for handling checkpoints data |
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53 | # @note This is not operational at the moment |
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54 | class CPT_file(Data_format): |
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55 | """Interface to native NetCDF format (.cpt) to be |
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56 | used for checkpointing (one day) |
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57 | """ |
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58 | |
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59 | ## |
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60 | # @brief Initialize this instantiation. |
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61 | # @param domain ?? |
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62 | # @param mode Mode of underlying data file (default WRITE). |
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63 | def __init__(self, domain, mode=netcdf_mode_w): |
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64 | from Scientific.IO.NetCDF import NetCDFFile |
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65 | |
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66 | self.precision = netcdf_float #Use full precision |
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67 | |
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68 | Data_format.__init__(self, domain, 'sww', mode) |
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69 | |
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70 | # NetCDF file definition |
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71 | fid = NetCDFFile(self.filename, mode) |
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72 | if mode[0] == 'w': |
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73 | # Create new file |
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74 | fid.institution = 'Geoscience Australia' |
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75 | fid.description = 'Checkpoint data' |
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76 | #fid.smooth = domain.smooth |
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77 | fid.order = domain.default_order |
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78 | |
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79 | # Dimension definitions |
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80 | fid.createDimension('number_of_volumes', self.number_of_volumes) |
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81 | fid.createDimension('number_of_vertices', 3) |
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82 | |
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83 | # Store info at all vertices (no smoothing) |
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84 | fid.createDimension('number_of_points', 3*self.number_of_volumes) |
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85 | fid.createDimension('number_of_timesteps', None) #extensible |
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86 | |
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87 | # Variable definitions |
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88 | |
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89 | # Mesh |
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90 | fid.createVariable('x', self.precision, ('number_of_points',)) |
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91 | fid.createVariable('y', self.precision, ('number_of_points',)) |
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92 | |
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93 | |
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94 | fid.createVariable('volumes', netcdf_int, ('number_of_volumes', |
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95 | 'number_of_vertices')) |
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96 | |
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97 | fid.createVariable('time', self.precision, ('number_of_timesteps',)) |
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98 | |
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99 | #Allocate space for all quantities |
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100 | for name in domain.quantities.keys(): |
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101 | fid.createVariable(name, self.precision, |
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102 | ('number_of_timesteps', |
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103 | 'number_of_points')) |
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104 | |
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105 | fid.close() |
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106 | |
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107 | ## |
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108 | # @brief Store connectivity data to underlying data file. |
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109 | def store_checkpoint(self): |
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110 | """Write x,y coordinates of triangles. |
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111 | Write connectivity ( |
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112 | constituting |
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113 | the bed elevation. |
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114 | """ |
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115 | |
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116 | from Scientific.IO.NetCDF import NetCDFFile |
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117 | |
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118 | domain = self.domain |
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119 | |
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120 | #Get NetCDF |
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121 | fid = NetCDFFile(self.filename, netcdf_mode_a) |
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122 | |
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123 | # Get the variables |
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124 | x = fid.variables['x'] |
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125 | y = fid.variables['y'] |
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126 | |
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127 | volumes = fid.variables['volumes'] |
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128 | |
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129 | # Get X, Y and bed elevation Z |
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130 | Q = domain.quantities['elevation'] |
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131 | X,Y,Z,V = Q.get_vertex_values(xy=True, precision=self.precision) |
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132 | |
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133 | x[:] = X.astype(self.precision) |
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134 | y[:] = Y.astype(self.precision) |
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135 | z[:] = Z.astype(self.precision) |
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136 | |
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137 | volumes[:] = V |
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138 | |
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139 | fid.close() |
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140 | |
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141 | ## |
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142 | # @brief Store time and named quantities to underlying data file. |
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143 | # @param name |
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144 | def store_timestep(self, name): |
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145 | """Store time and named quantity to file |
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146 | """ |
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147 | |
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148 | from Scientific.IO.NetCDF import NetCDFFile |
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149 | from time import sleep |
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150 | |
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151 | #Get NetCDF |
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152 | retries = 0 |
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153 | file_open = False |
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154 | while not file_open and retries < 10: |
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155 | try: |
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156 | fid = NetCDFFile(self.filename, netcdf_mode_a) |
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157 | except IOError: |
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158 | #This could happen if someone was reading the file. |
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159 | #In that case, wait a while and try again |
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160 | msg = 'Warning (store_timestep): File %s could not be opened' \ |
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161 | ' - trying again' % self.filename |
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162 | log.critical(msg) |
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163 | retries += 1 |
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164 | sleep(1) |
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165 | else: |
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166 | file_open = True |
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167 | |
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168 | if not file_open: |
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169 | msg = 'File %s could not be opened for append' % self.filename |
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170 | raise DataFileNotOpenError, msg |
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171 | |
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172 | domain = self.domain |
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173 | |
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174 | # Get the variables |
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175 | time = fid.variables['time'] |
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176 | stage = fid.variables['stage'] |
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177 | i = len(time) |
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178 | |
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179 | #Store stage |
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180 | time[i] = self.domain.time |
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181 | |
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182 | # Get quantity |
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183 | Q = domain.quantities[name] |
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184 | A,V = Q.get_vertex_values(xy=False, precision=self.precision) |
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185 | |
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186 | stage[i,:] = A.astype(self.precision) |
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187 | |
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188 | #Flush and close |
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189 | fid.sync() |
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190 | fid.close() |
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191 | |
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192 | |
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193 | class SWW_file(Data_format): |
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194 | """Interface to native NetCDF format (.sww) for storing model output |
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195 | |
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196 | There are two kinds of data |
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197 | |
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198 | 1: Constant data: Vertex coordinates and field values. Stored once |
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199 | 2: Variable data: Conserved quantities. Stored once per timestep. |
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200 | |
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201 | All data is assumed to reside at vertex locations. |
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202 | """ |
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203 | |
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204 | ## |
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205 | # @brief Instantiate this instance. |
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206 | # @param domain ?? |
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207 | # @param mode Mode of the underlying data file. |
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208 | # @param max_size ?? |
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209 | # @param recursion ?? |
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210 | # @note Prepare the underlying data file if mode starts with 'w'. |
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211 | def __init__(self, domain, |
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212 | mode=netcdf_mode_w, max_size=2000000000, recursion=False): |
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213 | from Scientific.IO.NetCDF import NetCDFFile |
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214 | |
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215 | self.precision = netcdf_float32 # Use single precision for quantities |
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216 | self.recursion = recursion |
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217 | self.mode = mode |
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218 | if hasattr(domain, 'max_size'): |
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219 | self.max_size = domain.max_size # File size max is 2Gig |
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220 | else: |
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221 | self.max_size = max_size |
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222 | if hasattr(domain, 'minimum_storable_height'): |
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223 | self.minimum_storable_height = domain.minimum_storable_height |
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224 | else: |
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225 | self.minimum_storable_height = default_minimum_storable_height |
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226 | |
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227 | # Call parent constructor |
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228 | Data_format.__init__(self, domain, 'sww', mode) |
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229 | |
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230 | # Get static and dynamic quantities from domain |
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231 | static_quantities = [] |
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232 | dynamic_quantities = [] |
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233 | |
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234 | for q in domain.quantities_to_be_stored: |
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235 | flag = domain.quantities_to_be_stored[q] |
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236 | |
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237 | msg = 'Quantity %s is requested to be stored ' % q |
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238 | msg += 'but it does not exist in domain.quantities' |
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239 | assert q in domain.quantities, msg |
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240 | |
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241 | assert flag in [1,2] |
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242 | if flag == 1: static_quantities.append(q) |
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243 | if flag == 2: dynamic_quantities.append(q) |
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244 | |
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245 | |
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246 | # NetCDF file definition |
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247 | fid = NetCDFFile(self.filename, mode) |
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248 | if mode[0] == 'w': |
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249 | description = 'Output from anuga.abstract_2d_finite_volumes ' \ |
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250 | 'suitable for plotting' |
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251 | |
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252 | self.writer = Write_sww(static_quantities, dynamic_quantities) |
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253 | self.writer.store_header(fid, |
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254 | domain.starttime, |
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255 | self.number_of_volumes, |
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256 | self.domain.number_of_full_nodes, |
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257 | description=description, |
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258 | smoothing=domain.smooth, |
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259 | order=domain.default_order, |
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260 | sww_precision=self.precision) |
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261 | |
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262 | # Extra optional information |
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263 | if hasattr(domain, 'texture'): |
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264 | fid.texture = domain.texture |
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265 | |
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266 | if domain.quantities_to_be_monitored is not None: |
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267 | fid.createDimension('singleton', 1) |
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268 | fid.createDimension('two', 2) |
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269 | |
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270 | poly = domain.monitor_polygon |
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271 | if poly is not None: |
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272 | N = len(poly) |
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273 | fid.createDimension('polygon_length', N) |
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274 | fid.createVariable('extrema.polygon', |
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275 | self.precision, |
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276 | ('polygon_length', 'two')) |
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277 | fid.variables['extrema.polygon'][:] = poly |
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278 | |
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279 | interval = domain.monitor_time_interval |
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280 | if interval is not None: |
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281 | fid.createVariable('extrema.time_interval', |
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282 | self.precision, |
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283 | ('two',)) |
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284 | fid.variables['extrema.time_interval'][:] = interval |
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285 | |
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286 | for q in domain.quantities_to_be_monitored: |
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287 | fid.createVariable(q + '.extrema', self.precision, |
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288 | ('numbers_in_range',)) |
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289 | fid.createVariable(q + '.min_location', self.precision, |
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290 | ('numbers_in_range',)) |
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291 | fid.createVariable(q + '.max_location', self.precision, |
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292 | ('numbers_in_range',)) |
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293 | fid.createVariable(q + '.min_time', self.precision, |
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294 | ('singleton',)) |
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295 | fid.createVariable(q + '.max_time', self.precision, |
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296 | ('singleton',)) |
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297 | |
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298 | fid.close() |
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299 | |
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300 | ## |
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301 | # @brief Store connectivity data into the underlying data file. |
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302 | def store_connectivity(self): |
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303 | """Store information about nodes, triangles and static quantities |
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304 | |
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305 | Writes x,y coordinates of triangles and their connectivity. |
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306 | |
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307 | Store also any quantity that has been identified as static. |
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308 | """ |
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309 | |
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310 | # FIXME: Change name to reflect the fact thta this function |
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311 | # stores both connectivity (triangulation) and static quantities |
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312 | |
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313 | from Scientific.IO.NetCDF import NetCDFFile |
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314 | |
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315 | domain = self.domain |
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316 | |
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317 | # append to the NetCDF file |
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318 | fid = NetCDFFile(self.filename, netcdf_mode_a) |
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319 | |
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320 | # Get X, Y from one (any) of the quantities |
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321 | Q = domain.quantities.values()[0] |
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322 | X,Y,_,V = Q.get_vertex_values(xy=True, precision=self.precision) |
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323 | |
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324 | # store the connectivity data |
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325 | points = num.concatenate((X[:,num.newaxis],Y[:,num.newaxis]), axis=1) |
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326 | self.writer.store_triangulation(fid, |
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327 | points, |
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328 | V.astype(num.float32), |
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329 | points_georeference=\ |
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330 | domain.geo_reference) |
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331 | |
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332 | |
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333 | # Get names of static quantities |
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334 | static_quantities = {} |
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335 | for name in self.writer.static_quantities: |
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336 | Q = domain.quantities[name] |
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337 | A, _ = Q.get_vertex_values(xy=False, |
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338 | precision=self.precision) |
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339 | static_quantities[name] = A |
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340 | |
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341 | # Store static quantities |
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342 | self.writer.store_static_quantities(fid, **static_quantities) |
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343 | |
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344 | fid.close() |
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345 | |
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346 | ## |
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347 | # @brief Store time and time dependent quantities |
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348 | # to the underlying data file. |
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349 | def store_timestep(self): |
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350 | """Store time and time dependent quantities |
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351 | """ |
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352 | |
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353 | from Scientific.IO.NetCDF import NetCDFFile |
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354 | import types |
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355 | from time import sleep |
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356 | from os import stat |
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357 | |
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358 | # Get NetCDF |
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359 | retries = 0 |
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360 | file_open = False |
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361 | while not file_open and retries < 10: |
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362 | try: |
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363 | # Open existing file |
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364 | fid = NetCDFFile(self.filename, netcdf_mode_a) |
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365 | except IOError: |
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366 | # This could happen if someone was reading the file. |
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367 | # In that case, wait a while and try again |
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368 | msg = 'Warning (store_timestep): File %s could not be opened' \ |
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369 | % self.filename |
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370 | msg += ' - trying step %s again' % self.domain.time |
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371 | log.critical(msg) |
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372 | retries += 1 |
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373 | sleep(1) |
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374 | else: |
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375 | file_open = True |
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376 | |
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377 | if not file_open: |
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378 | msg = 'File %s could not be opened for append' % self.filename |
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379 | raise DataFileNotOpenError, msg |
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380 | |
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381 | # Check to see if the file is already too big: |
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382 | time = fid.variables['time'] |
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383 | i = len(time) + 1 |
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384 | file_size = stat(self.filename)[6] |
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385 | file_size_increase = file_size / i |
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386 | if file_size + file_size_increase > self.max_size * 2**self.recursion: |
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387 | # In order to get the file name and start time correct, |
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388 | # I change the domain.filename and domain.starttime. |
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389 | # This is the only way to do this without changing |
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390 | # other modules (I think). |
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391 | |
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392 | # Write a filename addon that won't break the anuga viewers |
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393 | # (10.sww is bad) |
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394 | filename_ext = '_time_%s' % self.domain.time |
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395 | filename_ext = filename_ext.replace('.', '_') |
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396 | |
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397 | # Remember the old filename, then give domain a |
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398 | # name with the extension |
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399 | old_domain_filename = self.domain.get_name() |
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400 | if not self.recursion: |
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401 | self.domain.set_name(old_domain_filename + filename_ext) |
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402 | |
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403 | # Temporarily change the domain starttime to the current time |
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404 | old_domain_starttime = self.domain.starttime |
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405 | self.domain.starttime = self.domain.get_time() |
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406 | |
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407 | # Build a new data_structure. |
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408 | next_data_structure = SWW_file(self.domain, mode=self.mode, |
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409 | max_size=self.max_size, |
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410 | recursion=self.recursion+1) |
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411 | if not self.recursion: |
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412 | log.critical(' file_size = %s' % file_size) |
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413 | log.critical(' saving file to %s' |
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414 | % next_data_structure.filename) |
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415 | |
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416 | # Set up the new data_structure |
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417 | self.domain.writer = next_data_structure |
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418 | |
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419 | # Store connectivity and first timestep |
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420 | next_data_structure.store_connectivity() |
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421 | next_data_structure.store_timestep() |
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422 | fid.sync() |
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423 | fid.close() |
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424 | |
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425 | # Restore the old starttime and filename |
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426 | self.domain.starttime = old_domain_starttime |
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427 | self.domain.set_name(old_domain_filename) |
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428 | else: |
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429 | self.recursion = False |
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430 | domain = self.domain |
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431 | |
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432 | # Get the variables |
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433 | time = fid.variables['time'] |
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434 | i = len(time) |
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435 | |
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436 | if 'stage' in self.writer.dynamic_quantities: |
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437 | # Select only those values for stage, |
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438 | # xmomentum and ymomentum (if stored) where |
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439 | # depth exceeds minimum_storable_height |
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440 | # |
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441 | # In this branch it is assumed that elevation |
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442 | # is also available as a quantity |
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443 | |
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444 | Q = domain.quantities['stage'] |
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445 | w, _ = Q.get_vertex_values(xy=False) |
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446 | |
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447 | Q = domain.quantities['elevation'] |
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448 | z, _ = Q.get_vertex_values(xy=False) |
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449 | |
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450 | storable_indices = (w-z >= self.minimum_storable_height) |
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451 | else: |
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452 | # Very unlikely branch |
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453 | storable_indices = None # This means take all |
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454 | |
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455 | |
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456 | # Now store dynamic quantities |
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457 | dynamic_quantities = {} |
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458 | for name in self.writer.dynamic_quantities: |
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459 | netcdf_array = fid.variables[name] |
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460 | |
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461 | Q = domain.quantities[name] |
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462 | A, _ = Q.get_vertex_values(xy=False, |
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463 | precision=self.precision) |
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464 | |
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465 | if storable_indices is not None: |
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466 | if name == 'stage': |
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467 | A = num.choose(storable_indices, (z, A)) |
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468 | |
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469 | if name in ['xmomentum', 'ymomentum']: |
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470 | # Get xmomentum where depth exceeds |
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471 | # minimum_storable_height |
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472 | |
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473 | # Define a zero vector of same size and type as A |
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474 | # for use with momenta |
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475 | null = num.zeros(num.size(A), A.dtype.char) |
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476 | A = num.choose(storable_indices, (null, A)) |
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477 | |
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478 | dynamic_quantities[name] = A |
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479 | |
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480 | |
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481 | # Store dynamic quantities |
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482 | self.writer.store_quantities(fid, |
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483 | time=self.domain.time, |
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484 | sww_precision=self.precision, |
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485 | **dynamic_quantities) |
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486 | |
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487 | |
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488 | # Update extrema if requested |
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489 | domain = self.domain |
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490 | if domain.quantities_to_be_monitored is not None: |
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491 | for q, info in domain.quantities_to_be_monitored.items(): |
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492 | if info['min'] is not None: |
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493 | fid.variables[q + '.extrema'][0] = info['min'] |
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494 | fid.variables[q + '.min_location'][:] = \ |
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495 | info['min_location'] |
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496 | fid.variables[q + '.min_time'][0] = info['min_time'] |
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497 | |
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498 | if info['max'] is not None: |
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499 | fid.variables[q + '.extrema'][1] = info['max'] |
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500 | fid.variables[q + '.max_location'][:] = \ |
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501 | info['max_location'] |
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502 | fid.variables[q + '.max_time'][0] = info['max_time'] |
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503 | |
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504 | # Flush and close |
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505 | fid.sync() |
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506 | fid.close() |
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507 | |
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508 | |
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509 | ## |
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510 | # @brief Class to open an sww file so that domain can be populated with quantity values |
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511 | class Read_sww: |
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512 | |
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513 | def __init__(self, source): |
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514 | """The source parameter is assumed to be a NetCDF sww file. |
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515 | """ |
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516 | |
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517 | self.source = source |
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518 | |
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519 | self.frame_number = 0 |
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520 | |
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521 | fin = NetCDFFile(self.source, 'r') |
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522 | |
---|
523 | self.time = num.array(fin.variables['time'], num.float) |
---|
524 | self.last_frame_number = self.time.shape[0] - 1 |
---|
525 | |
---|
526 | self.frames = num.arange(self.last_frame_number+1) |
---|
527 | |
---|
528 | fin.close() |
---|
529 | |
---|
530 | self.read_mesh() |
---|
531 | |
---|
532 | self.quantities = {} |
---|
533 | |
---|
534 | self.read_quantities() |
---|
535 | |
---|
536 | |
---|
537 | def read_mesh(self): |
---|
538 | fin = NetCDFFile(self.source, 'r') |
---|
539 | |
---|
540 | self.vertices = num.array(fin.variables['volumes'], num.int) |
---|
541 | |
---|
542 | self.x = x = num.array(fin.variables['x'], num.float) |
---|
543 | self.y = y = num.array(fin.variables['y'], num.float) |
---|
544 | |
---|
545 | assert len(self.x) == len(self.y) |
---|
546 | |
---|
547 | self.xmin = num.min(x) |
---|
548 | self.xmax = num.max(x) |
---|
549 | self.ymin = num.min(y) |
---|
550 | self.ymax = num.max(y) |
---|
551 | |
---|
552 | |
---|
553 | |
---|
554 | fin.close() |
---|
555 | |
---|
556 | def read_quantities(self, frame_number=0): |
---|
557 | |
---|
558 | assert frame_number >= 0 and frame_number <= self.last_frame_number |
---|
559 | |
---|
560 | self.frame_number = frame_number |
---|
561 | |
---|
562 | M = len(self.x)/3 |
---|
563 | |
---|
564 | fin = NetCDFFile(self.source, 'r') |
---|
565 | |
---|
566 | for q in filter(lambda n:n != 'x' and n != 'y' and n != 'time' and n != 'volumes' and \ |
---|
567 | '_range' not in n, \ |
---|
568 | fin.variables.keys()): |
---|
569 | if len(fin.variables[q].shape) == 1: # Not a time-varying quantity |
---|
570 | self.quantities[q] = num.ravel(num.array(fin.variables[q], num.float)).reshape(M,3) |
---|
571 | else: # Time-varying, get the current timestep data |
---|
572 | self.quantities[q] = num.array(fin.variables[q][self.frame_number], num.float).reshape(M,3) |
---|
573 | fin.close() |
---|
574 | return self.quantities |
---|
575 | |
---|
576 | def get_bounds(self): |
---|
577 | return [self.xmin, self.xmax, self.ymin, self.ymax] |
---|
578 | |
---|
579 | def get_last_frame_number(self): |
---|
580 | return self.last_frame_number |
---|
581 | |
---|
582 | def get_time(self): |
---|
583 | return self.time[self.frame_number] |
---|
584 | |
---|
585 | |
---|
586 | # @brief A class to write an SWW file. |
---|
587 | class Write_sww: |
---|
588 | from anuga.shallow_water.shallow_water_domain import Domain |
---|
589 | |
---|
590 | RANGE = '_range' |
---|
591 | EXTREMA = ':extrema' |
---|
592 | |
---|
593 | ## |
---|
594 | # brief Instantiate the SWW writer class. |
---|
595 | def __init__(self, static_quantities, dynamic_quantities): |
---|
596 | """Initialise Write_sww with two list af quantity names: |
---|
597 | |
---|
598 | static_quantities (e.g. elevation or friction): |
---|
599 | Stored once at the beginning of the simulation in a 1D array |
---|
600 | of length number_of_points |
---|
601 | dynamic_quantities (e.g stage): |
---|
602 | Stored every timestep in a 2D array with |
---|
603 | dimensions number_of_points X number_of_timesteps |
---|
604 | |
---|
605 | """ |
---|
606 | self.static_quantities = static_quantities |
---|
607 | self.dynamic_quantities = dynamic_quantities |
---|
608 | |
---|
609 | |
---|
610 | ## |
---|
611 | # @brief Store a header in the SWW file. |
---|
612 | # @param outfile Open handle to the file that will be written. |
---|
613 | # @param times A list of time slices *or* a start time. |
---|
614 | # @param number_of_volumes The number of triangles. |
---|
615 | # @param number_of_points The number of points. |
---|
616 | # @param description The internal file description string. |
---|
617 | # @param smoothing True if smoothing is to be used. |
---|
618 | # @param order |
---|
619 | # @param sww_precision Data type of the quantity written (netcdf constant) |
---|
620 | # @param verbose True if this function is to be verbose. |
---|
621 | # @note If 'times' is a list, the info will be made relative. |
---|
622 | def store_header(self, |
---|
623 | outfile, |
---|
624 | times, |
---|
625 | number_of_volumes, |
---|
626 | number_of_points, |
---|
627 | description='Generated by ANUGA', |
---|
628 | smoothing=True, |
---|
629 | order=1, |
---|
630 | sww_precision=netcdf_float32, |
---|
631 | verbose=False): |
---|
632 | """Write an SWW file header. |
---|
633 | |
---|
634 | outfile - the open file that will be written |
---|
635 | times - A list of the time slice times OR a start time |
---|
636 | Note, if a list is given the info will be made relative. |
---|
637 | number_of_volumes - the number of triangles |
---|
638 | """ |
---|
639 | |
---|
640 | from anuga.abstract_2d_finite_volumes.util \ |
---|
641 | import get_revision_number |
---|
642 | |
---|
643 | outfile.institution = 'Geoscience Australia' |
---|
644 | outfile.description = description |
---|
645 | |
---|
646 | # For sww compatibility |
---|
647 | if smoothing is True: |
---|
648 | # Smoothing to be depreciated |
---|
649 | outfile.smoothing = 'Yes' |
---|
650 | outfile.vertices_are_stored_uniquely = 'False' |
---|
651 | else: |
---|
652 | # Smoothing to be depreciated |
---|
653 | outfile.smoothing = 'No' |
---|
654 | outfile.vertices_are_stored_uniquely = 'True' |
---|
655 | outfile.order = order |
---|
656 | |
---|
657 | try: |
---|
658 | revision_number = get_revision_number() |
---|
659 | except: |
---|
660 | # This will be triggered if the system cannot get the SVN |
---|
661 | # revision number. |
---|
662 | revision_number = None |
---|
663 | # Allow None to be stored as a string |
---|
664 | outfile.revision_number = str(revision_number) |
---|
665 | |
---|
666 | # This is being used to seperate one number from a list. |
---|
667 | # what it is actually doing is sorting lists from numeric arrays. |
---|
668 | if isinstance(times, (list, num.ndarray)): |
---|
669 | number_of_times = len(times) |
---|
670 | times = ensure_numeric(times) |
---|
671 | if number_of_times == 0: |
---|
672 | starttime = 0 |
---|
673 | else: |
---|
674 | starttime = times[0] |
---|
675 | times = times - starttime #Store relative times |
---|
676 | else: |
---|
677 | number_of_times = 0 |
---|
678 | starttime = times |
---|
679 | |
---|
680 | |
---|
681 | outfile.starttime = starttime |
---|
682 | |
---|
683 | # dimension definitions |
---|
684 | outfile.createDimension('number_of_volumes', number_of_volumes) |
---|
685 | outfile.createDimension('number_of_vertices', 3) |
---|
686 | outfile.createDimension('numbers_in_range', 2) |
---|
687 | |
---|
688 | if smoothing is True: |
---|
689 | outfile.createDimension('number_of_points', number_of_points) |
---|
690 | # FIXME(Ole): This will cause sww files for parallel domains to |
---|
691 | # have ghost nodes stored (but not used by triangles). |
---|
692 | # To clean this up, we have to change get_vertex_values and |
---|
693 | # friends in quantity.py (but I can't be bothered right now) |
---|
694 | else: |
---|
695 | outfile.createDimension('number_of_points', 3*number_of_volumes) |
---|
696 | |
---|
697 | outfile.createDimension('number_of_timesteps', number_of_times) |
---|
698 | |
---|
699 | # variable definitions |
---|
700 | outfile.createVariable('x', sww_precision, ('number_of_points',)) |
---|
701 | outfile.createVariable('y', sww_precision, ('number_of_points',)) |
---|
702 | |
---|
703 | outfile.createVariable('volumes', netcdf_int, ('number_of_volumes', |
---|
704 | 'number_of_vertices')) |
---|
705 | |
---|
706 | # Doing sww_precision instead of Float gives cast errors. |
---|
707 | outfile.createVariable('time', netcdf_float, |
---|
708 | ('number_of_timesteps',)) |
---|
709 | |
---|
710 | |
---|
711 | for q in self.static_quantities: |
---|
712 | |
---|
713 | outfile.createVariable(q, sww_precision, |
---|
714 | ('number_of_points',)) |
---|
715 | |
---|
716 | outfile.createVariable(q + Write_sww.RANGE, sww_precision, |
---|
717 | ('numbers_in_range',)) |
---|
718 | |
---|
719 | # Initialise ranges with small and large sentinels. |
---|
720 | # If this was in pure Python we could have used None sensibly |
---|
721 | outfile.variables[q+Write_sww.RANGE][0] = max_float # Min |
---|
722 | outfile.variables[q+Write_sww.RANGE][1] = -max_float # Max |
---|
723 | |
---|
724 | #if 'elevation' in self.static_quantities: |
---|
725 | # # FIXME: Backwards compat - get rid of z once old view has retired |
---|
726 | # outfile.createVariable('z', sww_precision, |
---|
727 | # ('number_of_points',)) |
---|
728 | |
---|
729 | for q in self.dynamic_quantities: |
---|
730 | outfile.createVariable(q, sww_precision, ('number_of_timesteps', |
---|
731 | 'number_of_points')) |
---|
732 | outfile.createVariable(q + Write_sww.RANGE, sww_precision, |
---|
733 | ('numbers_in_range',)) |
---|
734 | |
---|
735 | # Initialise ranges with small and large sentinels. |
---|
736 | # If this was in pure Python we could have used None sensibly |
---|
737 | outfile.variables[q+Write_sww.RANGE][0] = max_float # Min |
---|
738 | outfile.variables[q+Write_sww.RANGE][1] = -max_float # Max |
---|
739 | |
---|
740 | if isinstance(times, (list, num.ndarray)): |
---|
741 | outfile.variables['time'][:] = times # Store time relative |
---|
742 | |
---|
743 | if verbose: |
---|
744 | log.critical('------------------------------------------------') |
---|
745 | log.critical('Statistics:') |
---|
746 | log.critical(' t in [%f, %f], len(t) == %d' |
---|
747 | % (num.min(times), num.max(times), len(times.flat))) |
---|
748 | |
---|
749 | ## |
---|
750 | # @brief Store triangulation data in the underlying file. |
---|
751 | # @param outfile Open handle to underlying file. |
---|
752 | # @param points_utm List or array of points in UTM. |
---|
753 | # @param volumes |
---|
754 | # @param zone |
---|
755 | # @param new_origin georeference that the points can be set to. |
---|
756 | # @param points_georeference The georeference of the points_utm. |
---|
757 | # @param verbose True if this function is to be verbose. |
---|
758 | def store_triangulation(self, |
---|
759 | outfile, |
---|
760 | points_utm, |
---|
761 | volumes, |
---|
762 | zone=None, |
---|
763 | new_origin=None, |
---|
764 | points_georeference=None, |
---|
765 | verbose=False): |
---|
766 | """ |
---|
767 | new_origin - qa georeference that the points can be set to. (Maybe |
---|
768 | do this before calling this function.) |
---|
769 | |
---|
770 | points_utm - currently a list or array of the points in UTM. |
---|
771 | points_georeference - the georeference of the points_utm |
---|
772 | |
---|
773 | How about passing new_origin and current_origin. |
---|
774 | If you get both, do a convertion from the old to the new. |
---|
775 | |
---|
776 | If you only get new_origin, the points are absolute, |
---|
777 | convert to relative |
---|
778 | |
---|
779 | if you only get the current_origin the points are relative, store |
---|
780 | as relative. |
---|
781 | |
---|
782 | if you get no georefs create a new georef based on the minimums of |
---|
783 | points_utm. (Another option would be to default to absolute) |
---|
784 | |
---|
785 | Yes, and this is done in another part of the code. |
---|
786 | Probably geospatial. |
---|
787 | |
---|
788 | If you don't supply either geo_refs, then supply a zone. If not |
---|
789 | the default zone will be used. |
---|
790 | |
---|
791 | precon: |
---|
792 | header has been called. |
---|
793 | """ |
---|
794 | |
---|
795 | number_of_points = len(points_utm) |
---|
796 | volumes = num.array(volumes) |
---|
797 | points_utm = num.array(points_utm) |
---|
798 | |
---|
799 | # Given the two geo_refs and the points, do the stuff |
---|
800 | # described in the method header |
---|
801 | # if this is needed else where, pull out as a function |
---|
802 | points_georeference = ensure_geo_reference(points_georeference) |
---|
803 | new_origin = ensure_geo_reference(new_origin) |
---|
804 | if new_origin is None and points_georeference is not None: |
---|
805 | points = points_utm |
---|
806 | geo_ref = points_georeference |
---|
807 | else: |
---|
808 | if new_origin is None: |
---|
809 | new_origin = Geo_reference(zone, min(points_utm[:,0]), |
---|
810 | min(points_utm[:,1])) |
---|
811 | points = new_origin.change_points_geo_ref(points_utm, |
---|
812 | points_georeference) |
---|
813 | geo_ref = new_origin |
---|
814 | |
---|
815 | # At this stage I need a georef and points |
---|
816 | # the points are relative to the georef |
---|
817 | geo_ref.write_NetCDF(outfile) |
---|
818 | |
---|
819 | # This will put the geo ref in the middle |
---|
820 | #geo_ref = Geo_reference(refzone,(max(x)+min(x))/2.0,(max(x)+min(y))/2.) |
---|
821 | |
---|
822 | x = points[:,0] |
---|
823 | y = points[:,1] |
---|
824 | |
---|
825 | if verbose: |
---|
826 | log.critical('------------------------------------------------') |
---|
827 | log.critical('More Statistics:') |
---|
828 | log.critical(' Extent (/lon):') |
---|
829 | log.critical(' x in [%f, %f], len(lat) == %d' |
---|
830 | % (min(x), max(x), len(x))) |
---|
831 | log.critical(' y in [%f, %f], len(lon) == %d' |
---|
832 | % (min(y), max(y), len(y))) |
---|
833 | #log.critical(' z in [%f, %f], len(z) == %d' |
---|
834 | # % (min(elevation), max(elevation), len(elevation))) |
---|
835 | log.critical('geo_ref: %s' % str(geo_ref)) |
---|
836 | log.critical('------------------------------------------------') |
---|
837 | |
---|
838 | outfile.variables['x'][:] = points[:,0] #- geo_ref.get_xllcorner() |
---|
839 | outfile.variables['y'][:] = points[:,1] #- geo_ref.get_yllcorner() |
---|
840 | outfile.variables['volumes'][:] = volumes.astype(num.int32) #On Opteron 64 |
---|
841 | |
---|
842 | |
---|
843 | |
---|
844 | # @brief Write the static quantity data to the underlying file. |
---|
845 | # @param outfile Handle to open underlying file. |
---|
846 | # @param sww_precision Format of quantity data to write (default Float32). |
---|
847 | # @param verbose True if this function is to be verbose. |
---|
848 | # @param **quant |
---|
849 | def store_static_quantities(self, |
---|
850 | outfile, |
---|
851 | sww_precision=num.float32, |
---|
852 | verbose=False, |
---|
853 | **quant): |
---|
854 | """ |
---|
855 | Write the static quantity info. |
---|
856 | |
---|
857 | **quant is extra keyword arguments passed in. These must be |
---|
858 | the numpy arrays to be stored in the sww file at each timestep. |
---|
859 | |
---|
860 | The argument sww_precision allows for storing as either |
---|
861 | * single precision (default): num.float32 |
---|
862 | * double precision: num.float64 or num.float |
---|
863 | |
---|
864 | Precondition: |
---|
865 | store_triangulation and |
---|
866 | store_header have been called. |
---|
867 | """ |
---|
868 | |
---|
869 | # The dictionary quant must contain numpy arrays for each name. |
---|
870 | # These will typically be quantities from Domain such as friction |
---|
871 | # |
---|
872 | # Arrays not listed in static_quantitiues will be ignored, silently. |
---|
873 | # |
---|
874 | # This method will also write the ranges for each quantity, |
---|
875 | # e.g. stage_range, xmomentum_range and ymomentum_range |
---|
876 | for q in self.static_quantities: |
---|
877 | if not quant.has_key(q): |
---|
878 | msg = 'Values for quantity %s was not specified in ' % q |
---|
879 | msg += 'store_quantities so they cannot be stored.' |
---|
880 | raise NewQuantity, msg |
---|
881 | else: |
---|
882 | q_values = ensure_numeric(quant[q]) |
---|
883 | |
---|
884 | x = q_values.astype(sww_precision) |
---|
885 | outfile.variables[q][:] = x |
---|
886 | |
---|
887 | # This populates the _range values |
---|
888 | outfile.variables[q + Write_sww.RANGE][0] = num.min(x) |
---|
889 | outfile.variables[q + Write_sww.RANGE][1] = num.max(x) |
---|
890 | |
---|
891 | # FIXME: Hack for backwards compatibility with old viewer |
---|
892 | #if 'elevation' in self.static_quantities: |
---|
893 | # outfile.variables['z'][:] = outfile.variables['elevation'][:] |
---|
894 | |
---|
895 | |
---|
896 | |
---|
897 | |
---|
898 | |
---|
899 | ## |
---|
900 | # @brief Write the quantity data to the underlying file. |
---|
901 | # @param outfile Handle to open underlying file. |
---|
902 | # @param sww_precision Format of quantity data to write (default Float32). |
---|
903 | # @param slice_index |
---|
904 | # @param time |
---|
905 | # @param verbose True if this function is to be verbose. |
---|
906 | # @param **quant |
---|
907 | def store_quantities(self, |
---|
908 | outfile, |
---|
909 | sww_precision=num.float32, |
---|
910 | slice_index=None, |
---|
911 | time=None, |
---|
912 | verbose=False, |
---|
913 | **quant): |
---|
914 | """ |
---|
915 | Write the quantity info at each timestep. |
---|
916 | |
---|
917 | **quant is extra keyword arguments passed in. These must be |
---|
918 | the numpy arrays to be stored in the sww file at each timestep. |
---|
919 | |
---|
920 | if the time array is already been built, use the slice_index |
---|
921 | to specify the index. |
---|
922 | |
---|
923 | Otherwise, use time to increase the time dimension |
---|
924 | |
---|
925 | Maybe make this general, but the viewer assumes these quantities, |
---|
926 | so maybe we don't want it general - unless the viewer is general |
---|
927 | |
---|
928 | The argument sww_precision allows for storing as either |
---|
929 | * single precision (default): num.float32 |
---|
930 | * double precision: num.float64 or num.float |
---|
931 | |
---|
932 | Precondition: |
---|
933 | store_triangulation and |
---|
934 | store_header have been called. |
---|
935 | """ |
---|
936 | |
---|
937 | if time is not None: |
---|
938 | file_time = outfile.variables['time'] |
---|
939 | slice_index = len(file_time) |
---|
940 | file_time[slice_index] = time |
---|
941 | else: |
---|
942 | slice_index = int(slice_index) # Has to be cast in case it was numpy.int |
---|
943 | |
---|
944 | # Write the named dynamic quantities |
---|
945 | # The dictionary quant must contain numpy arrays for each name. |
---|
946 | # These will typically be the conserved quantities from Domain |
---|
947 | # (Typically stage, xmomentum, ymomentum). |
---|
948 | # |
---|
949 | # Arrays not listed in dynamic_quantitiues will be ignored, silently. |
---|
950 | # |
---|
951 | # This method will also write the ranges for each quantity, |
---|
952 | # e.g. stage_range, xmomentum_range and ymomentum_range |
---|
953 | for q in self.dynamic_quantities: |
---|
954 | if not quant.has_key(q): |
---|
955 | msg = 'Values for quantity %s was not specified in ' % q |
---|
956 | msg += 'store_quantities so they cannot be stored.' |
---|
957 | raise NewQuantity, msg |
---|
958 | else: |
---|
959 | q_values = ensure_numeric(quant[q]) |
---|
960 | |
---|
961 | x = q_values.astype(sww_precision) |
---|
962 | outfile.variables[q][slice_index] = x |
---|
963 | |
---|
964 | |
---|
965 | # This updates the _range values |
---|
966 | q_range = outfile.variables[q + Write_sww.RANGE][:] |
---|
967 | q_values_min = num.min(q_values) |
---|
968 | if q_values_min < q_range[0]: |
---|
969 | outfile.variables[q + Write_sww.RANGE][0] = q_values_min |
---|
970 | q_values_max = num.max(q_values) |
---|
971 | if q_values_max > q_range[1]: |
---|
972 | outfile.variables[q + Write_sww.RANGE][1] = q_values_max |
---|
973 | |
---|
974 | ## |
---|
975 | # @brief Print the quantities in the underlying file. |
---|
976 | # @param outfile UNUSED. |
---|
977 | def verbose_quantities(self, outfile): |
---|
978 | log.critical('------------------------------------------------') |
---|
979 | log.critical('More Statistics:') |
---|
980 | for q in self.dynamic_quantities: |
---|
981 | log.critical(' %s in [%f, %f]' |
---|
982 | % (q, outfile.variables[q+Write_sww.RANGE][0], |
---|
983 | outfile.variables[q+Write_sww.RANGE][1])) |
---|
984 | log.critical('------------------------------------------------') |
---|
985 | |
---|
986 | |
---|
987 | |
---|
988 | |
---|
989 | ## |
---|
990 | # @brief Get the extents of a NetCDF data file. |
---|
991 | # @param file_name The path to the SWW file. |
---|
992 | # @return A list of x, y, z and stage limits (min, max). |
---|
993 | def extent_sww(file_name): |
---|
994 | """Read in an sww file. |
---|
995 | |
---|
996 | Input: |
---|
997 | file_name - the sww file |
---|
998 | |
---|
999 | Output: |
---|
1000 | A list: [min(x),max(x),min(y),max(y),min(stage.flat),max(stage.flat)] |
---|
1001 | """ |
---|
1002 | |
---|
1003 | from Scientific.IO.NetCDF import NetCDFFile |
---|
1004 | |
---|
1005 | #Get NetCDF |
---|
1006 | fid = NetCDFFile(file_name, netcdf_mode_r) |
---|
1007 | |
---|
1008 | # Get the variables |
---|
1009 | x = fid.variables['x'][:] |
---|
1010 | y = fid.variables['y'][:] |
---|
1011 | stage = fid.variables['stage'][:] |
---|
1012 | |
---|
1013 | fid.close() |
---|
1014 | |
---|
1015 | return [min(x), max(x), min(y), max(y), num.min(stage), num.max(stage)] |
---|
1016 | |
---|
1017 | |
---|
1018 | ## |
---|
1019 | # @brief |
---|
1020 | # @param filename |
---|
1021 | # @param boundary |
---|
1022 | # @param t |
---|
1023 | # @param fail_if_NaN |
---|
1024 | # @param NaN_filler |
---|
1025 | # @param verbose |
---|
1026 | # @param very_verbose |
---|
1027 | # @return |
---|
1028 | def load_sww_as_domain(filename, boundary=None, t=None, |
---|
1029 | fail_if_NaN=True, NaN_filler=0, |
---|
1030 | verbose=False, very_verbose=False): |
---|
1031 | """ |
---|
1032 | Usage: domain = load_sww_as_domain('file.sww', |
---|
1033 | t=time (default = last time in file)) |
---|
1034 | |
---|
1035 | Boundary is not recommended if domain.smooth is not selected, as it |
---|
1036 | uses unique coordinates, but not unique boundaries. This means that |
---|
1037 | the boundary file will not be compatable with the coordinates, and will |
---|
1038 | give a different final boundary, or crash. |
---|
1039 | """ |
---|
1040 | |
---|
1041 | from Scientific.IO.NetCDF import NetCDFFile |
---|
1042 | from shallow_water import Domain |
---|
1043 | |
---|
1044 | # initialise NaN. |
---|
1045 | NaN = 9.969209968386869e+036 |
---|
1046 | |
---|
1047 | if verbose: log.critical('Reading from %s' % filename) |
---|
1048 | |
---|
1049 | fid = NetCDFFile(filename, netcdf_mode_r) # Open existing file for read |
---|
1050 | time = fid.variables['time'] # Timesteps |
---|
1051 | if t is None: |
---|
1052 | t = time[-1] |
---|
1053 | time_interp = get_time_interp(time,t) |
---|
1054 | |
---|
1055 | # Get the variables as numeric arrays |
---|
1056 | x = fid.variables['x'][:] # x-coordinates of vertices |
---|
1057 | y = fid.variables['y'][:] # y-coordinates of vertices |
---|
1058 | elevation = fid.variables['elevation'] # Elevation |
---|
1059 | stage = fid.variables['stage'] # Water level |
---|
1060 | xmomentum = fid.variables['xmomentum'] # Momentum in the x-direction |
---|
1061 | ymomentum = fid.variables['ymomentum'] # Momentum in the y-direction |
---|
1062 | |
---|
1063 | starttime = fid.starttime[0] |
---|
1064 | volumes = fid.variables['volumes'][:] # Connectivity |
---|
1065 | coordinates = num.transpose(num.asarray([x.tolist(), y.tolist()])) |
---|
1066 | # FIXME (Ole): Something like this might be better: |
---|
1067 | # concatenate((x, y), axis=1) |
---|
1068 | # or concatenate((x[:,num.newaxis], x[:,num.newaxis]), axis=1) |
---|
1069 | |
---|
1070 | conserved_quantities = [] |
---|
1071 | interpolated_quantities = {} |
---|
1072 | other_quantities = [] |
---|
1073 | |
---|
1074 | # get geo_reference |
---|
1075 | try: # sww files don't have to have a geo_ref |
---|
1076 | geo_reference = Geo_reference(NetCDFObject=fid) |
---|
1077 | except: # AttributeError, e: |
---|
1078 | geo_reference = None |
---|
1079 | |
---|
1080 | if verbose: log.critical(' getting quantities') |
---|
1081 | |
---|
1082 | for quantity in fid.variables.keys(): |
---|
1083 | dimensions = fid.variables[quantity].dimensions |
---|
1084 | if 'number_of_timesteps' in dimensions: |
---|
1085 | conserved_quantities.append(quantity) |
---|
1086 | interpolated_quantities[quantity] = \ |
---|
1087 | interpolated_quantity(fid.variables[quantity][:], time_interp) |
---|
1088 | else: |
---|
1089 | other_quantities.append(quantity) |
---|
1090 | |
---|
1091 | other_quantities.remove('x') |
---|
1092 | other_quantities.remove('y') |
---|
1093 | #other_quantities.remove('z') |
---|
1094 | other_quantities.remove('volumes') |
---|
1095 | try: |
---|
1096 | other_quantities.remove('stage_range') |
---|
1097 | other_quantities.remove('xmomentum_range') |
---|
1098 | other_quantities.remove('ymomentum_range') |
---|
1099 | other_quantities.remove('elevation_range') |
---|
1100 | except: |
---|
1101 | pass |
---|
1102 | |
---|
1103 | conserved_quantities.remove('time') |
---|
1104 | |
---|
1105 | if verbose: log.critical(' building domain') |
---|
1106 | |
---|
1107 | # From domain.Domain: |
---|
1108 | # domain = Domain(coordinates, volumes,\ |
---|
1109 | # conserved_quantities = conserved_quantities,\ |
---|
1110 | # other_quantities = other_quantities,zone=zone,\ |
---|
1111 | # xllcorner=xllcorner, yllcorner=yllcorner) |
---|
1112 | |
---|
1113 | # From shallow_water.Domain: |
---|
1114 | coordinates = coordinates.tolist() |
---|
1115 | volumes = volumes.tolist() |
---|
1116 | # FIXME:should this be in mesh? (peter row) |
---|
1117 | if fid.smoothing == 'Yes': |
---|
1118 | unique = False |
---|
1119 | else: |
---|
1120 | unique = True |
---|
1121 | if unique: |
---|
1122 | coordinates, volumes, boundary = weed(coordinates, volumes,boundary) |
---|
1123 | |
---|
1124 | |
---|
1125 | |
---|
1126 | try: |
---|
1127 | domain = Domain(coordinates, volumes, boundary) |
---|
1128 | except AssertionError, e: |
---|
1129 | fid.close() |
---|
1130 | msg = 'Domain could not be created: %s. ' \ |
---|
1131 | 'Perhaps use "fail_if_NaN=False and NaN_filler = ..."' % e |
---|
1132 | raise DataDomainError, msg |
---|
1133 | |
---|
1134 | if not boundary is None: |
---|
1135 | domain.boundary = boundary |
---|
1136 | |
---|
1137 | domain.geo_reference = geo_reference |
---|
1138 | |
---|
1139 | domain.starttime = float(starttime) + float(t) |
---|
1140 | domain.time = 0.0 |
---|
1141 | |
---|
1142 | for quantity in other_quantities: |
---|
1143 | try: |
---|
1144 | NaN = fid.variables[quantity].missing_value |
---|
1145 | except: |
---|
1146 | pass # quantity has no missing_value number |
---|
1147 | X = fid.variables[quantity][:] |
---|
1148 | if very_verbose: |
---|
1149 | log.critical(' %s' % str(quantity)) |
---|
1150 | log.critical(' NaN = %s' % str(NaN)) |
---|
1151 | log.critical(' max(X)') |
---|
1152 | log.critical(' %s' % str(max(X))) |
---|
1153 | log.critical(' max(X)==NaN') |
---|
1154 | log.critical(' %s' % str(max(X)==NaN)) |
---|
1155 | log.critical('') |
---|
1156 | if max(X) == NaN or min(X) == NaN: |
---|
1157 | if fail_if_NaN: |
---|
1158 | msg = 'quantity "%s" contains no_data entry' % quantity |
---|
1159 | raise DataMissingValuesError, msg |
---|
1160 | else: |
---|
1161 | data = (X != NaN) |
---|
1162 | X = (X*data) + (data==0)*NaN_filler |
---|
1163 | if unique: |
---|
1164 | X = num.resize(X, (len(X)/3, 3)) |
---|
1165 | domain.set_quantity(quantity, X) |
---|
1166 | # |
---|
1167 | for quantity in conserved_quantities: |
---|
1168 | try: |
---|
1169 | NaN = fid.variables[quantity].missing_value |
---|
1170 | except: |
---|
1171 | pass # quantity has no missing_value number |
---|
1172 | X = interpolated_quantities[quantity] |
---|
1173 | if very_verbose: |
---|
1174 | log.critical(' %s' % str(quantity)) |
---|
1175 | log.critical(' NaN = %s' % str(NaN)) |
---|
1176 | log.critical(' max(X)') |
---|
1177 | log.critical(' %s' % str(max(X))) |
---|
1178 | log.critical(' max(X)==NaN') |
---|
1179 | log.critical(' %s' % str(max(X)==NaN)) |
---|
1180 | log.critical('') |
---|
1181 | if max(X) == NaN or min(X) == NaN: |
---|
1182 | if fail_if_NaN: |
---|
1183 | msg = 'quantity "%s" contains no_data entry' % quantity |
---|
1184 | raise DataMissingValuesError, msg |
---|
1185 | else: |
---|
1186 | data = (X != NaN) |
---|
1187 | X = (X*data) + (data==0)*NaN_filler |
---|
1188 | if unique: |
---|
1189 | X = num.resize(X, (X.shape[0]/3, 3)) |
---|
1190 | domain.set_quantity(quantity, X) |
---|
1191 | |
---|
1192 | fid.close() |
---|
1193 | |
---|
1194 | return domain |
---|
1195 | |
---|
1196 | |
---|
1197 | ## |
---|
1198 | # @brief Get mesh and quantity data from an SWW file. |
---|
1199 | # @param filename Path to data file to read. |
---|
1200 | # @param quantities UNUSED! |
---|
1201 | # @param verbose True if this function is to be verbose. |
---|
1202 | # @return (mesh, quantities, time) where mesh is the mesh data, quantities is |
---|
1203 | # a dictionary of {name: value}, and time is the time vector. |
---|
1204 | # @note Quantities extracted: 'elevation', 'stage', 'xmomentum' and 'ymomentum' |
---|
1205 | def get_mesh_and_quantities_from_file(filename, |
---|
1206 | quantities=None, |
---|
1207 | verbose=False): |
---|
1208 | """Get and rebuild mesh structure and associated quantities from sww file |
---|
1209 | |
---|
1210 | Input: |
---|
1211 | filename - Name os sww file |
---|
1212 | quantities - Names of quantities to load |
---|
1213 | |
---|
1214 | Output: |
---|
1215 | mesh - instance of class Interpolate |
---|
1216 | (including mesh and interpolation functionality) |
---|
1217 | quantities - arrays with quantity values at each mesh node |
---|
1218 | time - vector of stored timesteps |
---|
1219 | |
---|
1220 | This function is used by e.g.: |
---|
1221 | get_interpolated_quantities_at_polyline_midpoints |
---|
1222 | """ |
---|
1223 | |
---|
1224 | # FIXME (Ole): Maybe refactor filefunction using this more fundamental code. |
---|
1225 | |
---|
1226 | import types |
---|
1227 | from Scientific.IO.NetCDF import NetCDFFile |
---|
1228 | from shallow_water import Domain |
---|
1229 | from anuga.abstract_2d_finite_volumes.neighbour_mesh import Mesh |
---|
1230 | |
---|
1231 | if verbose: log.critical('Reading from %s' % filename) |
---|
1232 | |
---|
1233 | fid = NetCDFFile(filename, netcdf_mode_r) # Open existing file for read |
---|
1234 | time = fid.variables['time'][:] # Time vector |
---|
1235 | time += fid.starttime[0] |
---|
1236 | |
---|
1237 | # Get the variables as numeric arrays |
---|
1238 | x = fid.variables['x'][:] # x-coordinates of nodes |
---|
1239 | y = fid.variables['y'][:] # y-coordinates of nodes |
---|
1240 | elevation = fid.variables['elevation'][:] # Elevation |
---|
1241 | stage = fid.variables['stage'][:] # Water level |
---|
1242 | xmomentum = fid.variables['xmomentum'][:] # Momentum in the x-direction |
---|
1243 | ymomentum = fid.variables['ymomentum'][:] # Momentum in the y-direction |
---|
1244 | |
---|
1245 | # Mesh (nodes (Mx2), triangles (Nx3)) |
---|
1246 | nodes = num.concatenate((x[:,num.newaxis], y[:,num.newaxis]), axis=1) |
---|
1247 | triangles = fid.variables['volumes'][:] |
---|
1248 | |
---|
1249 | # Get geo_reference |
---|
1250 | try: |
---|
1251 | geo_reference = Geo_reference(NetCDFObject=fid) |
---|
1252 | except: #AttributeError, e: |
---|
1253 | # Sww files don't have to have a geo_ref |
---|
1254 | geo_reference = None |
---|
1255 | |
---|
1256 | if verbose: log.critical(' building mesh from sww file %s' % filename) |
---|
1257 | |
---|
1258 | boundary = None |
---|
1259 | |
---|
1260 | #FIXME (Peter Row): Should this be in mesh? |
---|
1261 | if fid.smoothing != 'Yes': |
---|
1262 | nodes = nodes.tolist() |
---|
1263 | triangles = triangles.tolist() |
---|
1264 | nodes, triangles, boundary = weed(nodes, triangles, boundary) |
---|
1265 | |
---|
1266 | try: |
---|
1267 | mesh = Mesh(nodes, triangles, boundary, geo_reference=geo_reference) |
---|
1268 | except AssertionError, e: |
---|
1269 | fid.close() |
---|
1270 | msg = 'Domain could not be created: %s. "' % e |
---|
1271 | raise DataDomainError, msg |
---|
1272 | |
---|
1273 | quantities = {} |
---|
1274 | quantities['elevation'] = elevation |
---|
1275 | quantities['stage'] = stage |
---|
1276 | quantities['xmomentum'] = xmomentum |
---|
1277 | quantities['ymomentum'] = ymomentum |
---|
1278 | |
---|
1279 | fid.close() |
---|
1280 | |
---|
1281 | return mesh, quantities, time |
---|
1282 | |
---|
1283 | |
---|
1284 | |
---|
1285 | ## |
---|
1286 | # @brief |
---|
1287 | # @parm time |
---|
1288 | # @param t |
---|
1289 | # @return An (index, ration) tuple. |
---|
1290 | def get_time_interp(time, t=None): |
---|
1291 | #Finds the ratio and index for time interpolation. |
---|
1292 | #It is borrowed from previous abstract_2d_finite_volumes code. |
---|
1293 | if t is None: |
---|
1294 | t=time[-1] |
---|
1295 | index = -1 |
---|
1296 | ratio = 0. |
---|
1297 | else: |
---|
1298 | T = time |
---|
1299 | tau = t |
---|
1300 | index=0 |
---|
1301 | msg = 'Time interval derived from file %s [%s:%s]' \ |
---|
1302 | % ('FIXMEfilename', T[0], T[-1]) |
---|
1303 | msg += ' does not match model time: %s' % tau |
---|
1304 | if tau < time[0]: raise DataTimeError, msg |
---|
1305 | if tau > time[-1]: raise DataTimeError, msg |
---|
1306 | while tau > time[index]: index += 1 |
---|
1307 | while tau < time[index]: index -= 1 |
---|
1308 | if tau == time[index]: |
---|
1309 | #Protect against case where tau == time[-1] (last time) |
---|
1310 | # - also works in general when tau == time[i] |
---|
1311 | ratio = 0 |
---|
1312 | else: |
---|
1313 | #t is now between index and index+1 |
---|
1314 | ratio = (tau - time[index])/(time[index+1] - time[index]) |
---|
1315 | |
---|
1316 | return (index, ratio) |
---|
1317 | |
---|
1318 | |
---|
1319 | |
---|
1320 | ## |
---|
1321 | # @brief Interpolate a quantity wrt time. |
---|
1322 | # @param saved_quantity The quantity to interpolate. |
---|
1323 | # @param time_interp (index, ratio) |
---|
1324 | # @return A vector of interpolated values. |
---|
1325 | def interpolated_quantity(saved_quantity, time_interp): |
---|
1326 | '''Given an index and ratio, interpolate quantity with respect to time.''' |
---|
1327 | |
---|
1328 | index, ratio = time_interp |
---|
1329 | |
---|
1330 | Q = saved_quantity |
---|
1331 | |
---|
1332 | if ratio > 0: |
---|
1333 | q = (1-ratio)*Q[index] + ratio*Q[index+1] |
---|
1334 | else: |
---|
1335 | q = Q[index] |
---|
1336 | |
---|
1337 | #Return vector of interpolated values |
---|
1338 | return q |
---|
1339 | |
---|
1340 | |
---|
1341 | ## |
---|
1342 | # @brief |
---|
1343 | # @param coordinates |
---|
1344 | # @param volumes |
---|
1345 | # @param boundary |
---|
1346 | def weed(coordinates, volumes, boundary=None): |
---|
1347 | if isinstance(coordinates, num.ndarray): |
---|
1348 | coordinates = coordinates.tolist() |
---|
1349 | if isinstance(volumes, num.ndarray): |
---|
1350 | volumes = volumes.tolist() |
---|
1351 | |
---|
1352 | unique = False |
---|
1353 | point_dict = {} |
---|
1354 | same_point = {} |
---|
1355 | for i in range(len(coordinates)): |
---|
1356 | point = tuple(coordinates[i]) |
---|
1357 | if point_dict.has_key(point): |
---|
1358 | unique = True |
---|
1359 | same_point[i] = point |
---|
1360 | #to change all point i references to point j |
---|
1361 | else: |
---|
1362 | point_dict[point] = i |
---|
1363 | same_point[i] = point |
---|
1364 | |
---|
1365 | coordinates = [] |
---|
1366 | i = 0 |
---|
1367 | for point in point_dict.keys(): |
---|
1368 | point = tuple(point) |
---|
1369 | coordinates.append(list(point)) |
---|
1370 | point_dict[point] = i |
---|
1371 | i += 1 |
---|
1372 | |
---|
1373 | for volume in volumes: |
---|
1374 | for i in range(len(volume)): |
---|
1375 | index = volume[i] |
---|
1376 | if index > -1: |
---|
1377 | volume[i] = point_dict[same_point[index]] |
---|
1378 | |
---|
1379 | new_boundary = {} |
---|
1380 | if not boundary is None: |
---|
1381 | for segment in boundary.keys(): |
---|
1382 | point0 = point_dict[same_point[segment[0]]] |
---|
1383 | point1 = point_dict[same_point[segment[1]]] |
---|
1384 | label = boundary[segment] |
---|
1385 | #FIXME should the bounday attributes be concaterated |
---|
1386 | #('exterior, pond') or replaced ('pond')(peter row) |
---|
1387 | |
---|
1388 | if new_boundary.has_key((point0, point1)): |
---|
1389 | new_boundary[(point0,point1)] = new_boundary[(point0, point1)] |
---|
1390 | |
---|
1391 | elif new_boundary.has_key((point1, point0)): |
---|
1392 | new_boundary[(point1,point0)] = new_boundary[(point1, point0)] |
---|
1393 | else: new_boundary[(point0, point1)] = label |
---|
1394 | |
---|
1395 | boundary = new_boundary |
---|
1396 | |
---|
1397 | return coordinates, volumes, boundary |
---|
1398 | |
---|
1399 | |
---|
1400 | |
---|