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hderryhderry
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Merge branch 'feature/MosaicObj' of https://github.com/hderry/FMSgridtools into feature/MosaicObj
2 parents 45a7f9e + 7113843 commit 96699ab

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‎FMSgridtools/make_mosaic/__init__.py‎

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FMSgridtools/make_mosaic/empty.py renamed to FMSgridtools/make_mosaic/empty.py.orig

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‎FMSgridtools/make_mosaic/make_mosaic.py‎

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import click
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import solo_mosaic
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import regional_mosaic
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ATMOS_MOSAIC_HELP = "specify the atmosphere mosaic information \
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This file contains list of tile files which specify \
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the grid information for each tile. Each grid is \
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required to be logically rectangular grid. The \
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file name cannot be 'mosaic.nc'"
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TILE_FILE_HELP = "Grid file name of all tiles in the mosaic. \
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The file name should be the \
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relative path (exclude the absolute file path) \
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The absolute file path will be dir/tile_file. \
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the default for tile_file will be'horizontal_grid.tile#.nc'"
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mosaic_name = click.option('--mosaic_name',
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default='mosaic',
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help="mosaic name; The output file will be mosaic_name.nc.")
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sea_level = click.option('--sea_level', type=int, default=0)
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ocean_topog = click.option('--ocean_topog',
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type=click.Path(exists=True))
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@click.group()
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def make_mosaic():
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'''MAKE MOSAIC CLI'''
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@make_mosaic.command()
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@mosaic_name
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@click.option("--num_tiles",
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type=int,
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required=True,
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help="Number of tiles in the mosaic.")
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@click.option('--dir_name',
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type=click.Path(exists=True, file_okay=False),
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help="the directory that contains all the tile grid files." )
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@click.option('--tile_file', '-f',
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multiple=True, type=click.Path(exists=True, file_okay=True),
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help=TILE_FILE_HELP)
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@click.option('--periodx',
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default=0,
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help = "Specify the period in x-direction of mosaic. \
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Default value is 0 (not periodic)")
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@click.option('--periody', default=0,
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help="Specify the period in y-direction of mosaic. \
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Default value is 0 (not periodic)")
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def solo(num_tiles,
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dir_name,
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mosaic_name,
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tile_file,
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periodx,
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periody):
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solo_mosaic.make(num_tiles,
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dir_name,
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mosaic_name,
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tile_file,
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periodx,
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periody)
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@make_mosaic.command()
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@click.option('--global_mosaic',
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type=click.Path(exists=True),
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help="global_mosaic Specify the mosaic file for the global grid.")
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@click.option('--regional_file',
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type=click.Path(exists=True),
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help="regional_file Specify the regional model output file.")
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def regional(global_mosaic,
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regional_file):
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regional_mosaic.make(global_mosaic,
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regional_file)
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@make_mosaic.command()
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@mosaic_name
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@sea_level
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@ocean_topog
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@click.option('--input_mosaic',
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type=click.Path(exists=True))
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def quick(input_mosaic,
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mosaic_name,
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ocean_topog,
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sea_level,
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land_frac_file,
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land_frac_field):
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pass
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@make_mosaic.command()
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@mosaic_name
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@sea_level
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@ocean_topog
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@click.option('--atmos_mosaic',
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type=click.Path(exists=True),
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help = ATMOS_MOSAIC_HELP)
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@click.option('--ocean_mosaic',
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type=click.Path(exists=True))
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@click.option('--land_mosaic', type=click.Path(exists=True))
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@click.option('--wave_mosaic', type=click.Path(exists=True))
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@click.option('--interp_order', default=2)
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@click.option('--area_ratio_thresh', type=float, default=1e-6)
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@click.option('--check')
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@click.option('--rotate_poly')
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def coupler(atmos_mosaic,
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ocean_mosaic,
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ocean_topog,
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mosaic_name,
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sea_level,
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land_mosaic,
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wave_mosaic,
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interp_order,
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area_ratio_thresh,
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check,
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rotate_poly):
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pass
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#coupler.make(atmos_mosaic,
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# ocean_mosaic,
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# ocean_topog,
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# mosaic_name,
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# sea_level,
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# land_mosaic,
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# wave_mosaic,
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# interp_order,
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# area_ratio_thresh,
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# check
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# rotate_poly)
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if __name__ == '__main__':
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make_mosaic()

‎FMSgridtools/make_mosaic/regional_mosaic.py‎

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import sys
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import xarray as xr
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import numpy as np
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from FMSgridtools.shared.mosaicobj import MosaicObj
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def make(global_mosaic,
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regional_file):
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""" Generates a horizontal grid and solo mosaic for a regional output.
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The created grid and solo mosaic could be used to regrid regional
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output data onto regular lat-lon grid."""
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#get tile number from regional file
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try:
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tile = int(list(filter(str.isdigit, regional_file))[0])
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except IndexError:
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sys.exit("make_regional_mosaic: tile number not found in the regional_file name")
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ds = xr.open_dataset(regional_file)
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nx = ds.sizes['grid_xt_sub01']
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ny = ds.sizes['grid_yt_sub01']
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indx = ds.grid_xt_sub01.values
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indy = ds.grid_yt_sub01.values
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i_min = np.min(indx)
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i_max = np.max(indx)
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j_min = np.min(indy)
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j_max = np.max(indy)
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if i_max-i_min+1 != nx:
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print("Error: make_regional_mosaic: i_max-i_min+1 != nx")
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if j_max-j_min+1 != ny:
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print("Error: make_regional_mosaic: j_max-j_min+1 != ny")
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grid = MosaicObj(global_mosaic).griddict()
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try:
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x,y = grid[f'tile{tile}'].x, grid[f'tile{tile}'].y
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except KeyError:
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sys.exit("make_regional_mosaic: gridtile with matching tile number not found")
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xarr = x[round(2*j_min - 2):round(2*j_min - 2 + 2*ny+1), round(2*i_min - 2):round(2*i_min - 2 + 2*nx+1)]
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yarr = y[round(2*j_min - 2):round(2*j_min - 2 + 2*ny+1), round(2*i_min - 2):round(2*i_min - 2 + 2*nx+1)]
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outfile = f"regional_grid.tile{tile}.nc"
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write_out_regional_grid(tile, xarr,
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yarr, outfile)
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mosaic = "regional_mosaic.nc"
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regional_mosaic = MosaicObj(mosaic_name="regional_mosaic",
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gridfiles=np.array([outfile]),
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gridtiles=np.array([f"tile{tile}"]))
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regional_mosaic.write_out_regional_mosaic(mosaic)
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print("\nCongratulations: You have successfully run regional mosaic")
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def write_out_regional_grid(tile, xarr, yarr, outfile):
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tile = xr.DataArray(
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data=f'tile{tile}',
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attrs=dict(standard_name="grid_tile_spec")).astype('|S255')
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x = xr.DataArray(
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data=xarr,
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dims=["nyp", "nxp"],
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attrs=dict(
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standard_name="geographic_longitude", units="degree_east"))
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y = xr.DataArray(
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data=yarr,
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dims=["nyp", "nxp"],
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attrs=dict(
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standard_name="geographic_latitude", units="degree_north"))
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ds = xr.Dataset(
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data_vars={"tile": tile,
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"x": x,
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"y": y})
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encoding = {'x': {'_FillValue': None},
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'y': {'_FillValue': None}}
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ds.to_netcdf(outfile, encoding=encoding)
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‎FMSgridtools/make_mosaic/solo_mosaic.py‎

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import sys
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import numpy as np
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from FMSgridtools.shared.gridobj import GridObj
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from FMSgridtools.shared.mosaicobj import MosaicObj
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import pyfrenctools
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def make(num_tiles,
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dir_name,
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mosaic_name,
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tile_file,
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periodx,
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periody) -> None:
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"""Generates mosaic information between tiles. The mosaic information includes:
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list of tile files, list of contact region,
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specified by index, contact type."""
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contacts = []
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contact_index = []
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tilefiles = list(tile_file)
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nfiles = len(tilefiles)
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if nfiles == 0:
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if num_tiles == 1:
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tilefiles.append("horizontal_grid.tile1.nc")
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else:
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for n in range(num_tiles):
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tilefiles.append(f"horizontal_grid.tile{n}.nc")
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else:
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if nfiles != num_tiles:
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sys.exit("Error: number tiles provided through --ntiles"
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"does not match number of grid files passed through")
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gridtiles = [f'tile{i}' for i in range(1,nfiles+1)]
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grid = MosaicObj(ntiles=num_tiles, gridfiles = tilefiles,
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gridtiles = gridtiles).griddict()
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grid_data = {}
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for tile in gridtiles:
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grid_data[tile] = {}
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grid_data[tile]['x'] = grid[tile].x
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grid_data[tile]['y'] = grid[tile].y
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grid_data[tile]['nxp'] = grid[tile].nxp
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grid_data[tile]['nyp'] = grid[tile].nyp
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ncontact = 0
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#FIND CONTACT REGIONS
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for n in range(1,num_tiles):
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for m in range(n,num_tiles+1):
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contact = Contact(n, m, grid_data[f'tile{n}']['nxp'],
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grid_data[f'tile{m}']['nxp'],
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grid_data[f'tile{n}']['nyp'],
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grid_data[f'tile{m}']['nyp'],
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grid_data[f'tile{n}']['x'],
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grid_data[f'tile{m}']['x'],
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grid_data[f'tile{n}']['y'],
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grid_data[f'tile{m}']['y'],
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periodx, periody)
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count, istart1, iend1, jstart1, jend1, istart2, iend2, jstart2, jend2 = contact.align_contact()
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if count > 0:
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contacts.append(f"{mosaic_name}:tile{n}::{mosaic_name}:tile{m}")
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ncontact+=1
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contact_index.append(f"{istart1}:{iend1},{jstart1}:{jend1}::{istart2}:{iend2},{jstart2}:{jend2}")
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print("\nCongratulations: You have successfully run solo mosaic")
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print(f"NOTE: There are {ncontact} contacts\n")
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if ncontact > 0:
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mosaic = MosaicObj(mosaic_name=mosaic_name,
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gridlocation=dir_name,
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gridfiles=tilefiles,
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gridtiles=gridtiles,
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contacts=contacts,
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contact_index=contact_index)
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mosaic.write_out_mosaic(f'{mosaic_name}.nc')

‎FMSgridtools/shared/mosaicobj.py‎

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