| 1 | """ |
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| 2 | Merge a list of .sww files together into a single file. |
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| 3 | """ |
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| 4 | |
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| 5 | import numpy as num |
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| 6 | from anuga.utilities.numerical_tools import ensure_numeric |
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| 7 | |
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| 8 | from anuga.file.netcdf import NetCDFFile |
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| 9 | from anuga.config import netcdf_mode_r, netcdf_mode_w, netcdf_mode_a |
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| 10 | from anuga.config import netcdf_float, netcdf_float32, netcdf_int |
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| 11 | from anuga.file.sww import SWW_file, Write_sww |
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| 12 | |
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| 13 | def sww_merge(domain_global_name, np, verbose=False): |
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| 14 | |
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| 15 | output = domain_global_name+".sww" |
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| 16 | swwfiles = [ domain_global_name+"_P"+str(np)+"_"+str(v)+".sww" for v in range(np)] |
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| 17 | |
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| 18 | _sww_merge(swwfiles, output, verbose) |
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| 19 | |
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| 20 | |
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| 21 | def sww_merge_parallel(domain_global_name, np, verbose=False, delete_old=False): |
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| 22 | |
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| 23 | output = domain_global_name+".sww" |
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| 24 | swwfiles = [ domain_global_name+"_P"+str(np)+"_"+str(v)+".sww" for v in range(np)] |
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| 25 | |
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| 26 | fid = NetCDFFile(swwfiles[0], netcdf_mode_r) |
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| 27 | |
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| 28 | try: # works with netcdf4 |
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| 29 | number_of_volumes = len(fid.dimensions['number_of_volumes']) |
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| 30 | number_of_points = len(fid.dimensions['number_of_points']) |
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| 31 | except: # works with scientific.io.netcdf |
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| 32 | number_of_volumes = int(fid.dimensions['number_of_volumes']) |
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| 33 | number_of_points = int(fid.dimensions['number_of_points']) |
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| 34 | |
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| 35 | fid.close() |
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| 36 | |
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| 37 | if 3*number_of_volumes == number_of_points: |
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| 38 | _sww_merge_parallel_non_smooth(swwfiles, output, verbose, delete_old) |
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| 39 | else: |
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| 40 | _sww_merge_parallel_smooth(swwfiles, output, verbose, delete_old) |
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| 41 | |
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| 42 | |
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| 43 | def _sww_merge(swwfiles, output, verbose=False): |
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| 44 | """ |
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| 45 | Merge a list of sww files into a single file. |
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| 46 | |
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| 47 | May be useful for parallel runs. Note that colinear points and |
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| 48 | edges are not merged: there will essentially be multiple meshes within |
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| 49 | the one sww file. |
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| 50 | |
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| 51 | The sww files to be merged must have exactly the same timesteps. Note |
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| 52 | that some advanced information and custom quantities may not be |
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| 53 | exported. |
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| 54 | |
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| 55 | swwfiles is a list of .sww files to merge. |
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| 56 | output is the output filename, including .sww extension. |
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| 57 | verbose True to log output information |
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| 58 | """ |
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| 59 | |
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| 60 | if verbose: |
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| 61 | print "MERGING SWW Files" |
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| 62 | |
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| 63 | static_quantities = ['elevation'] |
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| 64 | dynamic_quantities = ['stage', 'xmomentum', 'ymomentum'] |
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| 65 | |
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| 66 | first_file = True |
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| 67 | tri_offset = 0 |
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| 68 | for filename in swwfiles: |
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| 69 | if verbose: |
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| 70 | print 'Reading file ', filename, ':' |
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| 71 | |
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| 72 | fid = NetCDFFile(filename, netcdf_mode_r) |
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| 73 | |
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| 74 | |
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| 75 | |
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| 76 | |
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| 77 | |
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| 78 | tris = fid.variables['volumes'][:] |
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| 79 | |
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| 80 | if first_file: |
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| 81 | times = fid.variables['time'][:] |
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| 82 | x = [] |
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| 83 | y = [] |
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| 84 | out_tris = list(tris) |
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| 85 | out_s_quantities = {} |
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| 86 | out_d_quantities = {} |
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| 87 | |
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| 88 | |
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| 89 | xllcorner = fid.xllcorner |
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| 90 | yllcorner = fid.yllcorner |
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| 91 | |
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| 92 | order = fid.order |
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| 93 | xllcorner = fid.xllcorner; |
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| 94 | yllcorner = fid.yllcorner ; |
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| 95 | zone = fid.zone; |
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| 96 | false_easting = fid.false_easting; |
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| 97 | false_northing = fid.false_northing; |
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| 98 | datum = fid.datum; |
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| 99 | projection = fid.projection; |
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| 100 | |
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| 101 | |
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| 102 | for quantity in static_quantities: |
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| 103 | out_s_quantities[quantity] = [] |
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| 104 | |
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| 105 | # Quantities are stored as a 2D array of timesteps x data. |
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| 106 | for quantity in dynamic_quantities: |
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| 107 | out_d_quantities[quantity] = [ [] for _ in range(len(times))] |
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| 108 | |
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| 109 | description = 'merged:' + getattr(fid, 'description') |
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| 110 | first_file = False |
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| 111 | else: |
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| 112 | for tri in tris: |
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| 113 | # Advance new tri indices to point at newly appended points. |
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| 114 | verts = [vertex+tri_offset for vertex in tri] |
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| 115 | out_tris.append(verts) |
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| 116 | |
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| 117 | |
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| 118 | |
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| 119 | try: # works with netcdf4 |
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| 120 | num_pts = len(fid.dimensions['number_of_points']) |
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| 121 | except: # works with scientific.io.netcdf |
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| 122 | num_pts = int(fid.dimensions['number_of_points']) |
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| 123 | |
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| 124 | tri_offset += num_pts |
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| 125 | |
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| 126 | if verbose: |
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| 127 | print ' new triangle index offset is ', tri_offset |
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| 128 | |
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| 129 | x.extend(list(fid.variables['x'][:])) |
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| 130 | y.extend(list(fid.variables['y'][:])) |
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| 131 | |
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| 132 | # Grow the list of static quantities associated with the x,y points |
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| 133 | for quantity in static_quantities: |
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| 134 | out_s_quantities[quantity].extend(fid.variables[quantity][:]) |
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| 135 | |
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| 136 | #Collate all dynamic quantities according to their timestep |
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| 137 | for quantity in dynamic_quantities: |
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| 138 | time_chunks = fid.variables[quantity][:] |
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| 139 | for i, time_chunk in enumerate(time_chunks): |
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| 140 | out_d_quantities[quantity][i].extend(time_chunk) |
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| 141 | |
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| 142 | # Mash all points into a single big list |
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| 143 | points = [[xx, yy] for xx, yy in zip(x, y)] |
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| 144 | |
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| 145 | points = num.asarray(points).astype(netcdf_float32) |
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| 146 | |
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| 147 | fid.close() |
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| 148 | |
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| 149 | #--------------------------- |
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| 150 | # Write out the SWW file |
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| 151 | #--------------------------- |
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| 152 | |
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| 153 | if verbose: |
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| 154 | print 'Writing file ', output, ':' |
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| 155 | fido = NetCDFFile(output, netcdf_mode_w) |
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| 156 | sww = Write_sww(static_quantities, dynamic_quantities) |
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| 157 | sww.store_header(fido, times, |
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| 158 | len(out_tris), |
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| 159 | len(points), |
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| 160 | description=description, |
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| 161 | sww_precision=netcdf_float32) |
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| 162 | |
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| 163 | |
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| 164 | |
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| 165 | from anuga.coordinate_transforms.geo_reference import Geo_reference |
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| 166 | geo_reference = Geo_reference() |
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| 167 | |
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| 168 | sww.store_triangulation(fido, points, out_tris, points_georeference=geo_reference) |
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| 169 | |
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| 170 | fido.order = order |
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| 171 | fido.xllcorner = xllcorner; |
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| 172 | fido.yllcorner = yllcorner ; |
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| 173 | fido.zone = zone; |
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| 174 | fido.false_easting = false_easting; |
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| 175 | fido.false_northing = false_northing; |
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| 176 | fido.datum = datum; |
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| 177 | fido.projection = projection; |
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| 178 | |
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| 179 | sww.store_static_quantities(fido, verbose=verbose, **out_s_quantities) |
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| 180 | |
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| 181 | # Write out all the dynamic quantities for each timestep |
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| 182 | for q in dynamic_quantities: |
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| 183 | q_values = out_d_quantities[q] |
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| 184 | for i, time_slice in enumerate(q_values): |
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| 185 | fido.variables[q][i] = num.array(time_slice, netcdf_float32) |
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| 186 | |
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| 187 | # This updates the _range values |
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| 188 | q_range = fido.variables[q + Write_sww.RANGE][:] |
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| 189 | q_values_min = num.min(q_values) |
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| 190 | if q_values_min < q_range[0]: |
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| 191 | fido.variables[q + Write_sww.RANGE][0] = q_values_min |
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| 192 | q_values_max = num.max(q_values) |
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| 193 | if q_values_max > q_range[1]: |
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| 194 | fido.variables[q + Write_sww.RANGE][1] = q_values_max |
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| 195 | |
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| 196 | |
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| 197 | fido.close() |
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| 198 | |
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| 199 | |
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| 200 | def _sww_merge_parallel_smooth(swwfiles, output, verbose=False, delete_old=False): |
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| 201 | """ |
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| 202 | Merge a list of sww files into a single file. |
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| 203 | |
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| 204 | Use to merge files created by parallel runs. |
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| 205 | |
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| 206 | The sww files to be merged must have exactly the same timesteps. |
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| 207 | |
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| 208 | It is assumed that the separate sww files have been stored in non_smooth |
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| 209 | format. |
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| 210 | |
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| 211 | Note that some advanced information and custom quantities may not be |
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| 212 | exported. |
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| 213 | |
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| 214 | swwfiles is a list of .sww files to merge. |
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| 215 | output is the output filename, including .sww extension. |
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| 216 | verbose True to log output information |
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| 217 | """ |
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| 218 | |
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| 219 | if verbose: |
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| 220 | print "MERGING SWW Files" |
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| 221 | |
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| 222 | |
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| 223 | first_file = True |
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| 224 | tri_offset = 0 |
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| 225 | for filename in swwfiles: |
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| 226 | if verbose: |
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| 227 | print 'Reading file ', filename, ':' |
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| 228 | |
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| 229 | fid = NetCDFFile(filename, netcdf_mode_r) |
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| 230 | |
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| 231 | if first_file: |
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| 232 | |
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| 233 | times = fid.variables['time'][:] |
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| 234 | n_steps = len(times) |
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| 235 | #number_of_timesteps = fid.dimensions['number_of_timesteps'] |
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| 236 | #print n_steps, number_of_timesteps |
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| 237 | starttime = int(fid.starttime) |
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| 238 | |
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| 239 | out_s_quantities = {} |
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| 240 | out_d_quantities = {} |
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| 241 | |
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| 242 | out_s_c_quantities = {} |
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| 243 | out_d_c_quantities = {} |
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| 244 | |
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| 245 | |
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| 246 | xllcorner = fid.xllcorner |
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| 247 | yllcorner = fid.yllcorner |
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| 248 | |
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| 249 | number_of_global_triangles = int(fid.number_of_global_triangles) |
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| 250 | number_of_global_nodes = int(fid.number_of_global_nodes) |
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| 251 | |
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| 252 | order = fid.order |
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| 253 | xllcorner = fid.xllcorner; |
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| 254 | yllcorner = fid.yllcorner ; |
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| 255 | zone = fid.zone; |
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| 256 | false_easting = fid.false_easting; |
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| 257 | false_northing = fid.false_northing; |
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| 258 | datum = fid.datum; |
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| 259 | projection = fid.projection; |
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| 260 | |
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| 261 | g_volumes = num.zeros((number_of_global_triangles,3),num.int) |
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| 262 | g_x = num.zeros((number_of_global_nodes,),num.float32) |
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| 263 | g_y = num.zeros((number_of_global_nodes,),num.float32) |
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| 264 | |
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| 265 | g_points = num.zeros((number_of_global_nodes,2),num.float32) |
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| 266 | |
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| 267 | #===================================== |
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| 268 | # Deal with the vertex based variables |
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| 269 | #===================================== |
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| 270 | quantities = set(['elevation', 'friction', 'stage', 'xmomentum', |
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| 271 | 'ymomentum', 'xvelocity', 'yvelocity', 'height']) |
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| 272 | variables = set(fid.variables.keys()) |
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| 273 | |
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| 274 | quantities = list(quantities & variables) |
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| 275 | |
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| 276 | static_quantities = [] |
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| 277 | dynamic_quantities = [] |
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| 278 | |
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| 279 | for quantity in quantities: |
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| 280 | # Test if quantity is static |
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| 281 | if n_steps == fid.variables[quantity].shape[0]: |
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| 282 | dynamic_quantities.append(quantity) |
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| 283 | else: |
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| 284 | static_quantities.append(quantity) |
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| 285 | |
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| 286 | for quantity in static_quantities: |
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| 287 | out_s_quantities[quantity] = num.zeros((number_of_global_nodes,),num.float32) |
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| 288 | |
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| 289 | # Quantities are stored as a 2D array of timesteps x data. |
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| 290 | for quantity in dynamic_quantities: |
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| 291 | out_d_quantities[quantity] = \ |
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| 292 | num.zeros((n_steps,number_of_global_nodes),num.float32) |
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| 293 | |
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| 294 | #======================================= |
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| 295 | # Deal with the centroid based variables |
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| 296 | #======================================= |
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| 297 | quantities = set(['elevation_c', 'friction_c', 'stage_c', 'xmomentum_c', |
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| 298 | 'ymomentum_c', 'xvelocity_c', 'yvelocity_c', 'height_c']) |
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| 299 | variables = set(fid.variables.keys()) |
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| 300 | |
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| 301 | quantities = list(quantities & variables) |
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| 302 | |
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| 303 | static_c_quantities = [] |
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| 304 | dynamic_c_quantities = [] |
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| 305 | |
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| 306 | for quantity in quantities: |
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| 307 | # Test if quantity is static |
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| 308 | if n_steps == fid.variables[quantity].shape[0]: |
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| 309 | dynamic_c_quantities.append(quantity) |
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| 310 | else: |
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| 311 | static_c_quantities.append(quantity) |
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| 312 | |
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| 313 | for quantity in static_c_quantities: |
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| 314 | out_s_c_quantities[quantity] = num.zeros((number_of_global_triangles,),num.float32) |
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| 315 | |
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| 316 | # Quantities are stored as a 2D array of timesteps x data. |
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| 317 | for quantity in dynamic_c_quantities: |
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| 318 | out_d_c_quantities[quantity] = \ |
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| 319 | num.zeros((n_steps,number_of_global_triangles),num.float32) |
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| 320 | |
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| 321 | description = 'merged:' + getattr(fid, 'description') |
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| 322 | first_file = False |
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| 323 | |
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| 324 | |
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| 325 | # Read in from files and add to global arrays |
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| 326 | |
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| 327 | tri_l2g = fid.variables['tri_l2g'][:] |
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| 328 | node_l2g = fid.variables['node_l2g'][:] |
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| 329 | tri_full_flag = fid.variables['tri_full_flag'][:] |
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| 330 | volumes = num.array(fid.variables['volumes'][:],dtype=num.int) |
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| 331 | l_volumes = num.zeros_like(volumes) |
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| 332 | l_old_volumes = num.zeros_like(volumes) |
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| 333 | |
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| 334 | |
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| 335 | # Change the local node ids to global id in the |
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| 336 | # volume array |
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| 337 | |
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| 338 | # FIXME SR: Surely we can knock up a numpy way of doing this |
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| 339 | #for i in range(len(l_volumes)): |
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| 340 | # g_n0 = node_l2g[volumes[i,0]] |
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| 341 | # g_n1 = node_l2g[volumes[i,1]] |
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| 342 | # g_n2 = node_l2g[volumes[i,2]] |
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| 343 | # |
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| 344 | # l_old_volumes[i,:] = [g_n0,g_n1,g_n2] |
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| 345 | |
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| 346 | g_n0 = node_l2g[volumes[:,0]].reshape(-1,1) |
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| 347 | g_n1 = node_l2g[volumes[:,1]].reshape(-1,1) |
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| 348 | g_n2 = node_l2g[volumes[:,2]].reshape(-1,1) |
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| 349 | |
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| 350 | #print g_n0.shape |
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| 351 | l_volumes = num.hstack((g_n0,g_n1,g_n2)) |
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| 352 | |
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| 353 | #assert num.allclose(l_volumes, l_old_volumes) |
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| 354 | |
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| 355 | # Just pick out the full triangles |
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| 356 | ftri_ids = num.where(tri_full_flag>0) |
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| 357 | ftri_l2g = num.compress(tri_full_flag, tri_l2g) |
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| 358 | |
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| 359 | #print l_volumes |
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| 360 | #print tri_full_flag |
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| 361 | #print tri_l2g |
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| 362 | #print ftri_l2g |
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| 363 | |
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| 364 | fg_volumes = num.compress(tri_full_flag,l_volumes,axis=0) |
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| 365 | g_volumes[ftri_l2g] = fg_volumes |
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| 366 | |
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| 367 | |
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| 368 | |
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| 369 | |
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| 370 | #g_x[node_l2g] = fid.variables['x'] |
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| 371 | #g_y[node_l2g] = fid.variables['y'] |
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| 372 | |
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| 373 | g_points[node_l2g,0] = fid.variables['x'] |
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| 374 | g_points[node_l2g,1] = fid.variables['y'] |
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| 375 | |
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| 376 | |
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| 377 | #print number_of_timesteps |
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| 378 | |
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| 379 | |
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| 380 | # FIXME SR: It seems that some of the "ghost" node quantity values |
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| 381 | # are being storded. We should only store those nodes which are associated with |
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| 382 | # full triangles. So we need an index array of "full" nodes, ie those in |
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| 383 | # full triangles |
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| 384 | |
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| 385 | #use numpy.compress and numpy.unique to get "full nodes |
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| 386 | |
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| 387 | f_volumes = num.compress(tri_full_flag,volumes,axis=0) |
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| 388 | fl_nodes = num.unique(f_volumes) |
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| 389 | f_node_l2g = node_l2g[fl_nodes] |
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| 390 | |
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| 391 | #print len(node_l2g) |
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| 392 | #print len(fl_nodes) |
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| 393 | |
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| 394 | # Read in static quantities |
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| 395 | for quantity in static_quantities: |
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| 396 | #out_s_quantities[quantity][node_l2g] = \ |
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| 397 | # num.array(fid.variables[quantity],dtype=num.float32) |
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| 398 | q = fid.variables[quantity] |
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| 399 | #print quantity, q.shape |
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| 400 | out_s_quantities[quantity][f_node_l2g] = \ |
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| 401 | num.array(q,dtype=num.float32)[fl_nodes] |
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| 402 | |
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| 403 | |
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| 404 | #Collate all dynamic quantities according to their timestep |
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| 405 | for quantity in dynamic_quantities: |
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| 406 | q = fid.variables[quantity] |
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| 407 | #print q.shape |
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| 408 | for i in range(n_steps): |
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| 409 | #out_d_quantities[quantity][i][node_l2g] = \ |
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| 410 | # num.array(q[i],dtype=num.float32) |
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| 411 | out_d_quantities[quantity][i][f_node_l2g] = \ |
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| 412 | num.array(q[i],dtype=num.float32)[fl_nodes] |
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| 413 | |
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| 414 | |
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| 415 | # Read in static c quantities |
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| 416 | for quantity in static_c_quantities: |
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| 417 | #out_s_quantities[quantity][node_l2g] = \ |
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| 418 | # num.array(fid.variables[quantity],dtype=num.float32) |
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| 419 | q = fid.variables[quantity] |
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| 420 | out_s_c_quantities[quantity][ftri_l2g] = \ |
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| 421 | num.array(q,dtype=num.float32)[ftri_ids] |
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| 422 | |
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| 423 | |
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| 424 | #Collate all dynamic c quantities according to their timestep |
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| 425 | for quantity in dynamic_c_quantities: |
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| 426 | q = fid.variables[quantity] |
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| 427 | #print q.shape |
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| 428 | for i in range(n_steps): |
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| 429 | out_d_c_quantities[quantity][i][ftri_l2g] = \ |
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| 430 | num.array(q[i],dtype=num.float32)[ftri_ids] |
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| 431 | |
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| 432 | |
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| 433 | fid.close() |
|---|
| 434 | |
|---|
| 435 | |
|---|
| 436 | #--------------------------- |
|---|
| 437 | # Write out the SWW file |
|---|
| 438 | #--------------------------- |
|---|
| 439 | #print g_points.shape |
|---|
| 440 | |
|---|
| 441 | #print number_of_global_triangles |
|---|
| 442 | #print number_of_global_nodes |
|---|
| 443 | |
|---|
| 444 | |
|---|
| 445 | if verbose: |
|---|
| 446 | print 'Writing file ', output, ':' |
|---|
| 447 | fido = NetCDFFile(output, netcdf_mode_w) |
|---|
| 448 | |
|---|
| 449 | sww = Write_sww(static_quantities, dynamic_quantities, static_c_quantities, dynamic_c_quantities) |
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| 450 | sww.store_header(fido, starttime, |
|---|
| 451 | number_of_global_triangles, |
|---|
| 452 | number_of_global_nodes, |
|---|
| 453 | description=description, |
|---|
| 454 | sww_precision=netcdf_float32) |
|---|
| 455 | |
|---|
| 456 | |
|---|
| 457 | |
|---|
| 458 | from anuga.coordinate_transforms.geo_reference import Geo_reference |
|---|
| 459 | geo_reference = Geo_reference() |
|---|
| 460 | |
|---|
| 461 | sww.store_triangulation(fido, g_points, g_volumes, points_georeference=geo_reference) |
|---|
| 462 | |
|---|
| 463 | fido.order = order |
|---|
| 464 | fido.xllcorner = xllcorner; |
|---|
| 465 | fido.yllcorner = yllcorner ; |
|---|
| 466 | fido.zone = zone; |
|---|
| 467 | fido.false_easting = false_easting; |
|---|
| 468 | fido.false_northing = false_northing; |
|---|
| 469 | fido.datum = datum; |
|---|
| 470 | fido.projection = projection; |
|---|
| 471 | |
|---|
| 472 | sww.store_static_quantities(fido, verbose=verbose, **out_s_quantities) |
|---|
| 473 | sww.store_static_quantities_centroid(fido, verbose=verbose, **out_s_c_quantities) |
|---|
| 474 | |
|---|
| 475 | # Write out all the dynamic quantities for each timestep |
|---|
| 476 | |
|---|
| 477 | for i in range(n_steps): |
|---|
| 478 | fido.variables['time'][i] = times[i] |
|---|
| 479 | |
|---|
| 480 | for q in dynamic_quantities: |
|---|
| 481 | q_values = out_d_quantities[q] |
|---|
| 482 | for i in range(n_steps): |
|---|
| 483 | fido.variables[q][i] = q_values[i] |
|---|
| 484 | |
|---|
| 485 | # This updates the _range values |
|---|
| 486 | q_range = fido.variables[q + Write_sww.RANGE][:] |
|---|
| 487 | q_values_min = num.min(q_values) |
|---|
| 488 | if q_values_min < q_range[0]: |
|---|
| 489 | fido.variables[q + Write_sww.RANGE][0] = q_values_min |
|---|
| 490 | q_values_max = num.max(q_values) |
|---|
| 491 | if q_values_max > q_range[1]: |
|---|
| 492 | fido.variables[q + Write_sww.RANGE][1] = q_values_max |
|---|
| 493 | |
|---|
| 494 | for q in dynamic_c_quantities: |
|---|
| 495 | q_values = out_d_c_quantities[q] |
|---|
| 496 | for i in range(n_steps): |
|---|
| 497 | fido.variables[q][i] = q_values[i] |
|---|
| 498 | |
|---|
| 499 | |
|---|
| 500 | #print out_s_quantities |
|---|
| 501 | #print out_d_quantities |
|---|
| 502 | |
|---|
| 503 | #print g_x |
|---|
| 504 | #print g_y |
|---|
| 505 | |
|---|
| 506 | #print g_volumes |
|---|
| 507 | |
|---|
| 508 | fido.close() |
|---|
| 509 | |
|---|
| 510 | if delete_old: |
|---|
| 511 | import os |
|---|
| 512 | for filename in swwfiles: |
|---|
| 513 | |
|---|
| 514 | if verbose: |
|---|
| 515 | print 'Deleting file ', filename, ':' |
|---|
| 516 | os.remove(filename) |
|---|
| 517 | |
|---|
| 518 | def _sww_merge_parallel_non_smooth(swwfiles, output, verbose=False, delete_old=False): |
|---|
| 519 | """ |
|---|
| 520 | Merge a list of sww files into a single file. |
|---|
| 521 | |
|---|
| 522 | Used to merge files created by parallel runs. |
|---|
| 523 | |
|---|
| 524 | The sww files to be merged must have exactly the same timesteps. |
|---|
| 525 | |
|---|
| 526 | It is assumed that the separate sww files have been stored in non_smooth |
|---|
| 527 | format. |
|---|
| 528 | |
|---|
| 529 | Note that some advanced information and custom quantities may not be |
|---|
| 530 | exported. |
|---|
| 531 | |
|---|
| 532 | swwfiles is a list of .sww files to merge. |
|---|
| 533 | output is the output filename, including .sww extension. |
|---|
| 534 | verbose True to log output information |
|---|
| 535 | """ |
|---|
| 536 | |
|---|
| 537 | if verbose: |
|---|
| 538 | print "MERGING SWW Files" |
|---|
| 539 | |
|---|
| 540 | |
|---|
| 541 | first_file = True |
|---|
| 542 | tri_offset = 0 |
|---|
| 543 | for filename in swwfiles: |
|---|
| 544 | if verbose: |
|---|
| 545 | print 'Reading file ', filename, ':' |
|---|
| 546 | |
|---|
| 547 | fid = NetCDFFile(filename, netcdf_mode_r) |
|---|
| 548 | |
|---|
| 549 | if first_file: |
|---|
| 550 | |
|---|
| 551 | times = fid.variables['time'][:] |
|---|
| 552 | n_steps = len(times) |
|---|
| 553 | number_of_timesteps = fid.dimensions['number_of_timesteps'] |
|---|
| 554 | #print n_steps, number_of_timesteps |
|---|
| 555 | starttime = int(fid.starttime) |
|---|
| 556 | |
|---|
| 557 | out_s_quantities = {} |
|---|
| 558 | out_d_quantities = {} |
|---|
| 559 | |
|---|
| 560 | |
|---|
| 561 | xllcorner = fid.xllcorner |
|---|
| 562 | yllcorner = fid.yllcorner |
|---|
| 563 | |
|---|
| 564 | number_of_global_triangles = int(fid.number_of_global_triangles) |
|---|
| 565 | number_of_global_nodes = int(fid.number_of_global_nodes) |
|---|
| 566 | number_of_global_triangle_vertices = 3*number_of_global_triangles |
|---|
| 567 | |
|---|
| 568 | |
|---|
| 569 | order = fid.order |
|---|
| 570 | xllcorner = fid.xllcorner; |
|---|
| 571 | yllcorner = fid.yllcorner ; |
|---|
| 572 | zone = fid.zone; |
|---|
| 573 | false_easting = fid.false_easting; |
|---|
| 574 | false_northing = fid.false_northing; |
|---|
| 575 | datum = fid.datum; |
|---|
| 576 | projection = fid.projection; |
|---|
| 577 | |
|---|
| 578 | g_volumes = num.arange(number_of_global_triangles*3).reshape(-1,3) |
|---|
| 579 | |
|---|
| 580 | |
|---|
| 581 | |
|---|
| 582 | g_x = num.zeros((number_of_global_triangle_vertices,),num.float32) |
|---|
| 583 | g_y = num.zeros((number_of_global_triangle_vertices,),num.float32) |
|---|
| 584 | |
|---|
| 585 | g_points = num.zeros((number_of_global_triangle_vertices,2),num.float32) |
|---|
| 586 | |
|---|
| 587 | |
|---|
| 588 | quantities = set(['elevation', 'friction', 'stage', 'xmomentum', |
|---|
| 589 | 'ymomentum', 'xvelocity', 'yvelocity', 'height']) |
|---|
| 590 | variables = set(fid.variables.keys()) |
|---|
| 591 | |
|---|
| 592 | quantities = list(quantities & variables) |
|---|
| 593 | |
|---|
| 594 | static_quantities = [] |
|---|
| 595 | dynamic_quantities = [] |
|---|
| 596 | |
|---|
| 597 | for quantity in quantities: |
|---|
| 598 | # Test if elevation is static |
|---|
| 599 | if n_steps == fid.variables[quantity].shape[0]: |
|---|
| 600 | dynamic_quantities.append(quantity) |
|---|
| 601 | else: |
|---|
| 602 | static_quantities.append(quantity) |
|---|
| 603 | |
|---|
| 604 | for quantity in static_quantities: |
|---|
| 605 | out_s_quantities[quantity] = num.zeros((3*number_of_global_triangles,),num.float32) |
|---|
| 606 | |
|---|
| 607 | # Quantities are stored as a 2D array of timesteps x data. |
|---|
| 608 | for quantity in dynamic_quantities: |
|---|
| 609 | out_d_quantities[quantity] = \ |
|---|
| 610 | num.zeros((n_steps,3*number_of_global_triangles),num.float32) |
|---|
| 611 | |
|---|
| 612 | description = 'merged:' + getattr(fid, 'description') |
|---|
| 613 | first_file = False |
|---|
| 614 | |
|---|
| 615 | |
|---|
| 616 | # Read in from files and add to global arrays |
|---|
| 617 | |
|---|
| 618 | tri_l2g = fid.variables['tri_l2g'][:] |
|---|
| 619 | node_l2g = fid.variables['node_l2g'][:] |
|---|
| 620 | tri_full_flag = fid.variables['tri_full_flag'][:] |
|---|
| 621 | |
|---|
| 622 | |
|---|
| 623 | |
|---|
| 624 | |
|---|
| 625 | f_ids = num.argwhere(tri_full_flag==1).reshape(-1,) |
|---|
| 626 | |
|---|
| 627 | f_gids = tri_l2g[f_ids] |
|---|
| 628 | |
|---|
| 629 | |
|---|
| 630 | g_vids = (3*f_gids.reshape(-1,1) + num.array([0,1,2])).reshape(-1,) |
|---|
| 631 | l_vids = (3*f_ids.reshape(-1,1) + num.array([0,1,2])).reshape(-1,) |
|---|
| 632 | |
|---|
| 633 | |
|---|
| 634 | l_x = num.array(fid.variables['x'][:],dtype=num.float32) |
|---|
| 635 | l_y = num.array(fid.variables['y'][:],dtype=num.float32) |
|---|
| 636 | |
|---|
| 637 | |
|---|
| 638 | g_x[g_vids] = l_x[l_vids] |
|---|
| 639 | g_y[g_vids] = l_y[l_vids] |
|---|
| 640 | |
|---|
| 641 | g_points[g_vids,0] = g_x[g_vids] |
|---|
| 642 | g_points[g_vids,1] = g_y[g_vids] |
|---|
| 643 | |
|---|
| 644 | |
|---|
| 645 | # Read in static quantities |
|---|
| 646 | for quantity in static_quantities: |
|---|
| 647 | #out_s_quantities[quantity][node_l2g] = \ |
|---|
| 648 | # num.array(fid.variables[quantity],dtype=num.float32) |
|---|
| 649 | q = fid.variables[quantity] |
|---|
| 650 | #print quantity, q.shape |
|---|
| 651 | out_s_quantities[quantity][g_vids] = \ |
|---|
| 652 | num.array(q,dtype=num.float32)[l_vids] |
|---|
| 653 | |
|---|
| 654 | |
|---|
| 655 | #Collate all dynamic quantities according to their timestep |
|---|
| 656 | for quantity in dynamic_quantities: |
|---|
| 657 | q = fid.variables[quantity] |
|---|
| 658 | #print q.shape |
|---|
| 659 | for i in range(n_steps): |
|---|
| 660 | #out_d_quantities[quantity][i][node_l2g] = \ |
|---|
| 661 | # num.array(q[i],dtype=num.float32) |
|---|
| 662 | out_d_quantities[quantity][i][g_vids] = \ |
|---|
| 663 | num.array(q[i],dtype=num.float32)[l_vids] |
|---|
| 664 | |
|---|
| 665 | |
|---|
| 666 | fid.close() |
|---|
| 667 | |
|---|
| 668 | #--------------------------- |
|---|
| 669 | # Write out the SWW file |
|---|
| 670 | #--------------------------- |
|---|
| 671 | |
|---|
| 672 | if verbose: |
|---|
| 673 | print 'Writing file ', output, ':' |
|---|
| 674 | |
|---|
| 675 | fido = NetCDFFile(output, netcdf_mode_w) |
|---|
| 676 | sww = Write_sww(static_quantities, dynamic_quantities) |
|---|
| 677 | sww.store_header(fido, starttime, |
|---|
| 678 | number_of_global_triangles, |
|---|
| 679 | number_of_global_triangles*3, |
|---|
| 680 | description=description, |
|---|
| 681 | sww_precision=netcdf_float32) |
|---|
| 682 | |
|---|
| 683 | |
|---|
| 684 | from anuga.coordinate_transforms.geo_reference import Geo_reference |
|---|
| 685 | geo_reference = Geo_reference() |
|---|
| 686 | |
|---|
| 687 | sww.store_triangulation(fido, g_points, g_volumes, points_georeference=geo_reference) |
|---|
| 688 | |
|---|
| 689 | fido.order = order |
|---|
| 690 | fido.xllcorner = xllcorner; |
|---|
| 691 | fido.yllcorner = yllcorner ; |
|---|
| 692 | fido.zone = zone; |
|---|
| 693 | fido.false_easting = false_easting; |
|---|
| 694 | fido.false_northing = false_northing; |
|---|
| 695 | fido.datum = datum; |
|---|
| 696 | fido.projection = projection; |
|---|
| 697 | |
|---|
| 698 | sww.store_static_quantities(fido, verbose=verbose, **out_s_quantities) |
|---|
| 699 | |
|---|
| 700 | # Write out all the dynamic quantities for each timestep |
|---|
| 701 | |
|---|
| 702 | for i in range(n_steps): |
|---|
| 703 | fido.variables['time'][i] = times[i] |
|---|
| 704 | |
|---|
| 705 | for q in dynamic_quantities: |
|---|
| 706 | q_values = out_d_quantities[q] |
|---|
| 707 | for i in range(n_steps): |
|---|
| 708 | fido.variables[q][i] = q_values[i] |
|---|
| 709 | |
|---|
| 710 | # This updates the _range values |
|---|
| 711 | q_range = fido.variables[q + Write_sww.RANGE][:] |
|---|
| 712 | q_values_min = num.min(q_values) |
|---|
| 713 | if q_values_min < q_range[0]: |
|---|
| 714 | fido.variables[q + Write_sww.RANGE][0] = q_values_min |
|---|
| 715 | q_values_max = num.max(q_values) |
|---|
| 716 | if q_values_max > q_range[1]: |
|---|
| 717 | fido.variables[q + Write_sww.RANGE][1] = q_values_max |
|---|
| 718 | |
|---|
| 719 | |
|---|
| 720 | fido.close() |
|---|
| 721 | |
|---|
| 722 | if delete_old: |
|---|
| 723 | import os |
|---|
| 724 | for filename in swwfiles: |
|---|
| 725 | |
|---|
| 726 | if verbose: |
|---|
| 727 | print 'Deleting file ', filename, ':' |
|---|
| 728 | os.remove(filename) |
|---|
| 729 | |
|---|
| 730 | |
|---|
| 731 | |
|---|
| 732 | |
|---|
| 733 | |
|---|
| 734 | |
|---|
| 735 | if __name__ == "__main__": |
|---|
| 736 | |
|---|
| 737 | import argparse |
|---|
| 738 | from anuga.anuga_exceptions import ANUGAError |
|---|
| 739 | |
|---|
| 740 | |
|---|
| 741 | parser = argparse.ArgumentParser(description='Merge sww files created from parallel run') |
|---|
| 742 | parser.add_argument('-np', type=int, default = 4, |
|---|
| 743 | help='number of processors used to produce sww files') |
|---|
| 744 | parser.add_argument('-f', type=str, default="domain", |
|---|
| 745 | help='domain global name') |
|---|
| 746 | parser.add_argument('-v', nargs='?', type=bool, const=True, default=False, |
|---|
| 747 | help='verbosity') |
|---|
| 748 | parser.add_argument('-delete_old', nargs='?', type=bool, const=True, default=False, |
|---|
| 749 | help='Flag to delete the input files') |
|---|
| 750 | args = parser.parse_args() |
|---|
| 751 | |
|---|
| 752 | np = args.np |
|---|
| 753 | domain_global_name = args.f |
|---|
| 754 | verbose = args.v |
|---|
| 755 | delete_old = args.delete_old |
|---|
| 756 | |
|---|
| 757 | |
|---|
| 758 | try: |
|---|
| 759 | sww_merge_parallel(domain_global_name, np, verbose, delete_old) |
|---|
| 760 | except: |
|---|
| 761 | msg = 'ERROR: When merging sww files %s '% domain_global_name |
|---|
| 762 | print msg |
|---|
| 763 | raise |
|---|
