Mercurial > repos > climate > mean_per_zone

annotate zonal_statistics.py @ 1:639192aa63f5 draft default tip

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planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit a5d176b7d0dc81bae07569d396edced43cfa2702
author climate
date Mon, 24 Jun 2019 02:41:08 -0400
parents 40727a2668d6
children
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40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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1 #!/usr/bin/env python3
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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3 import argparse
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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4 import warnings
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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6 import geopandas
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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8 import matplotlib as mpl
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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9 mpl.use('Agg')
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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10 from matplotlib import pyplot # noqa: I202,E402
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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12 import pandas as pd # noqa: I202,E402
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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14 from rasterstats import zonal_stats # noqa: I202,E402
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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16 import xarray as xr # noqa: I202,E402
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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19 if __name__ == '__main__':
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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20 warnings.filterwarnings("ignore")
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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21 parser = argparse.ArgumentParser()
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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22 parser.add_argument(
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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23 'raster',
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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24 help='input raster file with geographical coordinates (netCDF format)'
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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25 )
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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27 parser.add_argument(
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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28 'shapefile', help='input shapefile name with polygons '
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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29 )
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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31 parser.add_argument(
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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32 'variable', help='name of the variable in raster file'
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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33 )
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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34 parser.add_argument(
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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35 'output', help='output filename to store resulting image (png format)'
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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36 )
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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37 parser.add_argument(
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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38 '-s', '--stat', help='type of statistics [min, max, mean, count]'
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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39 )
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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40 parser.add_argument(
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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41 '-t', '--title', help='title for the generated plot'
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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42 )
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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43 parser.add_argument("-v", "--verbose", help="switch on verbose mode",
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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44 action="store_true")
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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45
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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46 args = parser.parse_args()
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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47 if args.stat is None:
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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48 stat_type = 'mean'
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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49 else:
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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50 stat_type = args.stat
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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51
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52 dset = xr.open_dataset(args.raster)
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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53 dset[args.variable].to_netcdf(".tmp.nc")
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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54 zs = zonal_stats(args.shapefile, ".tmp.nc", stats=stat_type)
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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55 df_zonal_stats = pd.DataFrame(zs)
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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56 world = geopandas.read_file(args.shapefile)
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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57 df = pd.concat([world, df_zonal_stats], axis=1)
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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58 ddf = df.dropna()
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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59 f, ax = pyplot.subplots(1, figsize=(20, 10))
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60
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61 visu = ddf.plot(column=stat_type, scheme='Quantiles', k=15, cmap='jet',
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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62 legend=True, ax=ax,
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63 legend_kwds={'loc': 'lower left',
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64 'frameon': True,
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65 'title': args.variable,
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66 'bbox_to_anchor': (1, 0.05)
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67 }
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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68 ) # plot done
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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69 ax.set_xlabel("Longitude")
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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70 ax.set_ylabel("Latitude")
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71
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72 if args.title is None:
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73 f.suptitle(stat_type + " computed over areas")
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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74 else:
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75 f.suptitle(args.title)
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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76 if args.verbose:
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77 print("plot generated")
40727a2668d6 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/mean-per-zone commit 24f20e7459e275c14376680f9bb91cd8ac26d9a5
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78
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79 pyplot.savefig(args.output, format='png')