Mercurial > repos > ecology > xarray_netcdf2netcdf

annotate xarray_tool.py @ 2:e87073edecd6 draft

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"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
author ecology
date Thu, 20 Jan 2022 17:08:29 +0000
parents b0780241f916
children
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2
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
1 # xarray tool for:
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
2 # - getting metadata information
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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3 # - select data and save results in csv file for further post-processing
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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4
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
5 import argparse
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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6 import csv
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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7 import os
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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8 import warnings
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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9
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
10 import geopandas as gdp
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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11
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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12 import pandas as pd
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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13
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
14 from shapely.geometry import Point
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
15 from shapely.ops import nearest_points
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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16
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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17 import xarray as xr
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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19
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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20 class XarrayTool ():
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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21 def __init__(self, infile, outfile_info="", outfile_summary="",
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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22 select="", outfile="", outputdir="", latname="",
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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23 latvalN="", latvalS="", lonname="", lonvalE="",
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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24 lonvalW="", filter_list="", coords="", time="",
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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25 verbose=False, no_missing=False, coords_info=None,
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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26 tolerance=None):
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
27 self.infile = infile
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
28 self.outfile_info = outfile_info
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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29 self.outfile_summary = outfile_summary
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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30 self.select = select
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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31 self.outfile = outfile
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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32 self.outputdir = outputdir
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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33 self.latname = latname
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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34 if tolerance != "" and tolerance is not None:
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
35 self.tolerance = float(tolerance)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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36 else:
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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37 self.tolerance = -1
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
38 if latvalN != "" and latvalN is not None:
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
39 self.latvalN = float(latvalN)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
40 else:
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
41 self.latvalN = ""
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
42 if latvalS != "" and latvalS is not None:
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
43 self.latvalS = float(latvalS)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
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44 else:
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
45 self.latvalS = ""
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
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46 self.lonname = lonname
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
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47 if lonvalE != "" and lonvalE is not None:
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
48 self.lonvalE = float(lonvalE)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
49 else:
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
50 self.lonvalE = ""
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
51 if lonvalW != "" and lonvalW is not None:
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
52 self.lonvalW = float(lonvalW)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
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53 else:
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
54 self.lonvalW = ""
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
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55 self.filter = filter_list
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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56 self.time = time
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
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57 self.coords = coords
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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58 self.verbose = verbose
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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59 self.no_missing = no_missing
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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60 # initialization
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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61 self.dset = None
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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62 self.gset = None
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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63 self.coords_info = coords_info
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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64 if self.verbose:
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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65 print("infile: ", self.infile)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
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66 print("outfile_info: ", self.outfile_info)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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67 print("outfile_summary: ", self.outfile_summary)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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68 print("outfile: ", self.outfile)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
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69 print("select: ", self.select)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
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70 print("outfile: ", self.outfile)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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71 print("outputdir: ", self.outputdir)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
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72 print("latname: ", self.latname)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
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73 print("latvalN: ", self.latvalN)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
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74 print("latvalS: ", self.latvalS)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
75 print("lonname: ", self.lonname)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
76 print("lonvalE: ", self.lonvalE)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
77 print("lonvalW: ", self.lonvalW)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
78 print("filter: ", self.filter)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
79 print("time: ", self.time)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
80 print("coords: ", self.coords)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
81 print("coords_info: ", self.coords_info)
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
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82
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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83 def info(self):
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84 f = open(self.outfile_info, 'w')
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85 ds = xr.open_dataset(self.infile)
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86 ds.info(f)
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87 f.close()
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88
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89 def summary(self):
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90 f = open(self.outfile_summary, 'w')
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91 ds = xr.open_dataset(self.infile)
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92 writer = csv.writer(f, delimiter='\t')
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93 header = ['VariableName', 'NumberOfDimensions']
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94 for idx, val in enumerate(ds.dims.items()):
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95 header.append('Dim' + str(idx) + 'Name')
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96 header.append('Dim' + str(idx) + 'Size')
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97 writer.writerow(header)
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98 for name, da in ds.data_vars.items():
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99 line = [name]
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100 line.append(len(ds[name].shape))
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101 for d, s in zip(da.shape, da.sizes):
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102 line.append(s)
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103 line.append(d)
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104 writer.writerow(line)
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105 for name, da in ds.coords.items():
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106 line = [name]
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107 line.append(len(ds[name].shape))
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108 for d, s in zip(da.shape, da.sizes):
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109 line.append(s)
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110 line.append(d)
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111 writer.writerow(line)
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112 f.close()
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113
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114 def rowfilter(self, single_filter):
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115 split_filter = single_filter.split('#')
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116 filter_varname = split_filter[0]
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117 op = split_filter[1]
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118 ll = float(split_filter[2])
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119 if (op == 'bi'):
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120 rl = float(split_filter[3])
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121 if filter_varname == self.select:
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122 # filter on values of the selected variable
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123 if op == 'bi':
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124 self.dset = self.dset.where(
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125 (self.dset <= rl) & (self.dset >= ll)
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126 )
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127 elif op == 'le':
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128 self.dset = self.dset.where(self.dset <= ll)
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129 elif op == 'ge':
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130 self.dset = self.dset.where(self.dset >= ll)
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131 elif op == 'e':
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132 self.dset = self.dset.where(self.dset == ll)
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133 else: # filter on other dimensions of the selected variable
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134 if op == 'bi':
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135 self.dset = self.dset.sel({filter_varname: slice(ll, rl)})
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136 elif op == 'le':
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137 self.dset = self.dset.sel({filter_varname: slice(None, ll)})
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138 elif op == 'ge':
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139 self.dset = self.dset.sel({filter_varname: slice(ll, None)})
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140 elif op == 'e':
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141 self.dset = self.dset.sel({filter_varname: ll},
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142 method='nearest')
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143
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144 def selection(self):
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145 if self.dset is None:
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146 self.ds = xr.open_dataset(self.infile)
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147 self.dset = self.ds[self.select] # select variable
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148 if self.time:
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149 self.datetime_selection()
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150 if self.filter:
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151 self.filter_selection()
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152
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153 self.area_selection()
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154 if self.gset.count() > 1:
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155 # convert to dataframe if several rows and cols
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156 self.gset = self.gset.to_dataframe().dropna(how='all'). \
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157 reset_index()
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158 self.gset.to_csv(self.outfile, header=True, sep='\t')
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159 else:
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160 data = {
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161 self.latname: [self.gset[self.latname].values],
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162 self.lonname: [self.gset[self.lonname].values],
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163 self.select: [self.gset.values]
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164 }
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165
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166 df = pd.DataFrame(data, columns=[self.latname, self.lonname,
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167 self.select])
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168 df.to_csv(self.outfile, header=True, sep='\t')
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169
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170 def datetime_selection(self):
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171 split_filter = self.time.split('#')
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172 time_varname = split_filter[0]
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173 op = split_filter[1]
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174 ll = split_filter[2]
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175 if (op == 'sl'):
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176 rl = split_filter[3]
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177 self.dset = self.dset.sel({time_varname: slice(ll, rl)})
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178 elif (op == 'to'):
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179 self.dset = self.dset.sel({time_varname: slice(None, ll)})
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180 elif (op == 'from'):
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181 self.dset = self.dset.sel({time_varname: slice(ll, None)})
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182 elif (op == 'is'):
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183 self.dset = self.dset.sel({time_varname: ll}, method='nearest')
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184
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185 def filter_selection(self):
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186 for single_filter in self.filter:
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187 self.rowfilter(single_filter)
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188
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189 def area_selection(self):
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190
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191 if self.latvalS != "" and self.lonvalW != "":
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192 # Select geographical area
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193 self.gset = self.dset.sel({self.latname:
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194 slice(self.latvalS, self.latvalN),
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195 self.lonname:
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196 slice(self.lonvalW, self.lonvalE)})
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197 elif self.latvalN != "" and self.lonvalE != "":
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198 # select nearest location
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199 if self.no_missing:
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200 self.nearest_latvalN = self.latvalN
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201 self.nearest_lonvalE = self.lonvalE
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202 else:
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203 # find nearest location without NaN values
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204 self.nearest_location()
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205 if self.tolerance > 0:
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206 self.gset = self.dset.sel({self.latname: self.nearest_latvalN,
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207 self.lonname: self.nearest_lonvalE},
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208 method='nearest',
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209 tolerance=self.tolerance)
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210 else:
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211 self.gset = self.dset.sel({self.latname: self.nearest_latvalN,
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212 self.lonname: self.nearest_lonvalE},
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213 method='nearest')
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214 else:
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215 self.gset = self.dset
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216
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217 def nearest_location(self):
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218 # Build a geopandas dataframe with all first elements in each dimension
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219 # so we assume null values correspond to a mask that is the same for
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220 # all dimensions in the dataset.
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221 dsel_frame = self.dset
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222 for dim in self.dset.dims:
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223 if dim != self.latname and dim != self.lonname:
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224 dsel_frame = dsel_frame.isel({dim: 0})
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225 # transform to pandas dataframe
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226 dff = dsel_frame.to_dataframe().dropna().reset_index()
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227 # transform to geopandas to collocate
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228 gdf = gdp.GeoDataFrame(dff,
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229 geometry=gdp.points_from_xy(dff[self.lonname],
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230 dff[self.latname]))
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231 # Find nearest location where values are not null
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232 point = Point(self.lonvalE, self.latvalN)
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233 multipoint = gdf.geometry.unary_union
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234 queried_geom, nearest_geom = nearest_points(point, multipoint)
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235 self.nearest_latvalN = nearest_geom.y
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236 self.nearest_lonvalE = nearest_geom.x
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237
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238 def selection_from_coords(self):
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239 fcoords = pd.read_csv(self.coords, sep='\t')
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240 for row in fcoords.itertuples():
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241 self.latvalN = row[0]
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242 self.lonvalE = row[1]
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243 self.outfile = (os.path.join(self.outputdir,
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244 self.select + '_' +
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245 str(row.Index) + '.tabular'))
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246 self.selection()
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247
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248 def get_coords_info(self):
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diff changeset
249 ds = xr.open_dataset(self.infile)
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ecology
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diff changeset
250 for c in ds.coords:
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ecology
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diff changeset
251 filename = os.path.join(self.coords_info,
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
252 c.strip() +
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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253 '.tabular')
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ecology
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diff changeset
254 pd = ds.coords[c].to_pandas()
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ecology
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diff changeset
255 pd.index = range(len(pd))
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ecology
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diff changeset
256 pd.to_csv(filename, header=False, sep='\t')
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ecology
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257
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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258
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
259 if __name__ == '__main__':
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ecology
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diff changeset
260 warnings.filterwarnings("ignore")
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ecology
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diff changeset
261 parser = argparse.ArgumentParser()
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
262
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
263 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
264 'infile',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
265 help='netCDF input filename'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
266 )
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
267 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
268 '--info',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
269 help='Output filename where metadata information is stored'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
270 )
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
271 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
272 '--summary',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
273 help='Output filename where data summary information is stored'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
274 )
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
275 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
276 '--select',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
277 help='Variable name to select'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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278 )
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
279 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
280 '--latname',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
281 help='Latitude name'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
282 )
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
283 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
284 '--latvalN',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
285 help='North latitude value'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
286 )
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
287 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
288 '--latvalS',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
289 help='South latitude value'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
290 )
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
291 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
292 '--lonname',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
293 help='Longitude name'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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294 )
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
295 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
296 '--lonvalE',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
297 help='East longitude value'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
298 )
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
299 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
300 '--lonvalW',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
301 help='West longitude value'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
302 )
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
303 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
304 '--tolerance',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
305 help='Maximum distance between original and selected value for '
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
306 ' inexact matches e.g. abs(index[indexer] - target) <= tolerance'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
307 )
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
308 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
309 '--coords',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
310 help='Input file containing Latitude and Longitude'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
311 'for geographical selection'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
312 )
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
313 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
314 '--coords_info',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
315 help='output-folder where for each coordinate, coordinate values '
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
316 ' are being printed in the corresponding outputfile'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
317 )
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
318 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
319 '--filter',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
320 nargs="*",
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
321 help='Filter list variable#operator#value_s#value_e'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
322 )
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
323 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
324 '--time',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
parents: 0
diff changeset
325 help='select timeseries variable#operator#value_s[#value_e]'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
326 )
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
327 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
328 '--outfile',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
329 help='csv outfile for storing results of the selection'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
330 '(valid only when --select)'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
331 )
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
332 parser.add_argument(
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
333 '--outputdir',
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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diff changeset
334 help='folder name for storing results with multiple selections'
e87073edecd6 "planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"
ecology
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335 '(valid only when --select)'
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336 )
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337 parser.add_argument(
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338 "-v", "--verbose",
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339 help="switch on verbose mode",
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340 action="store_true"
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341 )
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342 parser.add_argument(
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343 "--no_missing",
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344 help="""Do not take into account possible null/missing values
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345 (only valid for single location)""",
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346 action="store_true"
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347 )
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348 args = parser.parse_args()
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349
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350 p = XarrayTool(args.infile, args.info, args.summary, args.select,
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351 args.outfile, args.outputdir, args.latname,
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352 args.latvalN, args.latvalS, args.lonname,
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353 args.lonvalE, args.lonvalW, args.filter,
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354 args.coords, args.time, args.verbose,
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355 args.no_missing, args.coords_info, args.tolerance)
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356 if args.info:
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357 p.info()
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358 if args.summary:
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359 p.summary()
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360 if args.coords:
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361 p.selection_from_coords()
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362 elif args.select:
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363 p.selection()
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364 elif args.coords_info:
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365 p.get_coords_info()