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annotate psymap_simple.py @ 3:b7dcc1cb0871 draft default tip

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planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 526396eeef506a7a8b868d9663b9cde0bcab83ab
author climate
date Tue, 01 Oct 2024 20:11:36 +0000
parents 533c276ae533
children
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eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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1 #!/usr/bin/env python3
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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2 #
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3 #
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4 # usage: psymap_simple.py [-h] [--proj PROJ]
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5 # [--cmap CMAP]
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6 # [--output OUTPUT]
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7 # [-l]
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8 # [-v]
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9 # input varname
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10 #
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11 # positional arguments:
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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12 # input input filename with geographical coordinates (netCDF
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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13 # format)
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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14 # varname Specify which variable to plot (case sensitive)
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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15 #
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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16 # optional arguments:
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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17 # -h, --help show this help message and exit
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18 # -l, --logscale log scale the data
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19 # --proj PROJ Specify the projection on which we draw
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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20 # --cmap CMAP Specify which colormap to use for plotting
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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21 # --output OUTPUT output filename to store resulting image (png format)
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22 # --time TIMES time index from the file for multiple plots ("0 1 2 3")
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23 # --nrow NROW number of rows for multiple plot grid
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24 # --ncol NCOL number of columns for multiple plot grid
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25 # --format date format such as %Y (for year) %B (for month), etc.
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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26 # --title plot or subplot title
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eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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27 # -v, --verbose switch on verbose mode
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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28 #
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29
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30 import argparse
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31 import math
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32 import warnings
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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33 from pathlib import Path
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34
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35 import matplotlib as mpl
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36 import psyplot.project as psy # noqa: I202,E402
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37 import xarray
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38
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39 mpl.use('Agg')
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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40 from matplotlib import pyplot # noqa: I202,E402
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41 from psyplot import rcParams # noqa: I202,E402
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42
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43
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44 class PsyPlot ():
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45 def __init__(self, input, varname, output=None, logscale=False, cmap=None,
533c276ae533 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
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46 proj=None, verbose=False, time=None, nrow=None, ncol=None,
533c276ae533 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
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47 format=None, title=None):
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48 self.input = input
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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49 self.varname = varname
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50 if proj is None or proj == "":
533c276ae533 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
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51 self.proj = "cyl"
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52 else:
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53 self.proj = proj
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54 self.cmap = cmap if cmap is not None else "jet"
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55 self.time = time if time is not None else []
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56 self.ncol = int(ncol) if ncol is not None else int(1)
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57 self.nrow = int(nrow) if nrow is not None else int(1)
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58
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59 # Open dataset
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60 ds = xarray.open_dataset(input)[varname]
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61 minv = math.log2(ds.data.min())
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62 maxv = math.log2(ds.data.max())
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63 if title is not None:
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64 self.title = title
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65 else:
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66 self.title = ds.long_name
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67 if len(self.title) > 60:
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68 self.title = ds.standard_name
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69 del ds
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70
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71 if logscale:
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72 # Check that data range is sufficient for log scaling
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73 if maxv < (minv * (10.0 ** 2.0)):
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74 print("Not possible to log scale, switching to linear scale")
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75 self.bounds = None
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76 else:
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77 self.bounds = ['log', 2]
533c276ae533 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
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78 else:
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79 self.bounds = None
1
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80 if format is None:
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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81 self.format = ""
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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82 else:
2
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83 self.format = "%B %e, %Y"
0
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84 if output is None:
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85 self.output = Path(input).stem + '.png'
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86 else:
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87 self.output = output
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88 if verbose:
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89 print("input: ", self.input)
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90 print("proj: ", self.proj)
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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diff changeset
91 print("varname: ", self.varname)
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parents:
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92 print("cmap: ", self.cmap)
1
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parents: 0
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93 print("time: ", self.time)
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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parents: 0
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94 print("ncol: ", self.ncol)
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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parents: 0
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95 print("nrow: ", self.nrow)
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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parents: 0
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96 print("title: ", self.title)
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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parents: 0
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97 print("date format: ", self.format)
2
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parents: 1
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98 print("logscale: ", self.bounds)
0
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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parents:
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99 print("output: ", self.output)
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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parents:
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100
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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parents:
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101 def plot(self):
2
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102 clabel = '{desc}'
1
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103 if self.title and self.format:
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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104 title = self.title + "\n" + self.format
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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parents: 0
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105 elif not self.title and self.format:
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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parents: 0
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106 title = self.format
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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parents: 0
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107 elif self.title and not self.format:
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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parents: 0
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108 title = self.title
2
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parents: 1
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109 clabel = self.title
1
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110
2
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111 # Plot with chosen options
533c276ae533 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
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112 if self.bounds is None:
0
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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parents:
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113 psy.plot.mapplot(self.input, name=self.varname,
eb1f3666ce17 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit c1362af034361b6fb869411f1ea928388f230d72
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114 cmap=self.cmap,
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parents:
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115 projection=self.proj,
1
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116 title=title,
2
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117 clabel=clabel)
533c276ae533 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
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118 else:
533c276ae533 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
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parents: 1
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119 psy.plot.mapplot(self.input, name=self.varname,
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120 cmap=self.cmap, bounds=self.bounds,
533c276ae533 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
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parents: 1
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121 projection=self.proj,
533c276ae533 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
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122 title=title,
533c276ae533 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
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parents: 1
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123 clabel=clabel)
0
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124
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parents:
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125 pyplot.savefig(self.output)
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126
1
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parents: 0
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127 def multiple_plot(self):
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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128 if not self.format:
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129 self.format = "%B %e, %Y"
0
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130
1
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131 if not self.title:
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132 title = self.format
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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133 else:
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parents: 0
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134 title = self.title + "\n" + self.format
2
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135
1
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136 mpl.rcParams['figure.figsize'] = [20, 8]
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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137 mpl.rcParams.update({'font.size': 8})
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138 rcParams.update({'plotter.maps.grid_labelsize': 8.0})
2
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139
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140 # Plot using options
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141 if self.bounds is None:
1
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142 m = psy.plot.mapplot(self.input, name=self.varname,
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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143 cmap=self.cmap,
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144 projection=self.proj,
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145 ax=(self.nrow, self.ncol),
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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146 time=self.time, sort=['time'],
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147 title=title,
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148 clabel='{desc}')
2
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149 else:
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150 m = psy.plot.mapplot(self.input, name=self.varname,
533c276ae533 planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit d330adb8ea0000ffb2e1dcc2346fd34409f6618e
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151 cmap=self.cmap, bounds=self.bounds,
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152 projection=self.proj,
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153 ax=(self.nrow, self.ncol),
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154 time=self.time, sort=['time'],
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155 title=title,
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156 clabel='{desc}')
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157
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158 m.share(keys='bounds')
1
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159
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160 pyplot.savefig(self.output)
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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161
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162
2
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parents: 1
diff changeset
163 def psymap_plot(input, proj, varname, logscale, cmap, output, verbose, time,
1
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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parents: 0
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164 nrow, ncol, format, title):
0
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parents:
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165 """Generate plot from input filename"""
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166
2
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diff changeset
167 p = PsyPlot(input, varname, output, logscale, cmap, proj, verbose, time,
1
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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168 nrow, ncol, format, title)
2
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169
1
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parents: 0
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170 if len(time) == 0:
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171 p.plot()
322e000d8c48 "planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
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parents: 0
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172 else:
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diff changeset
173 p.multiple_plot()
0
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174
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175
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parents:
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176 if __name__ == '__main__':
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parents:
diff changeset
177 warnings.filterwarnings("ignore")
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parents:
diff changeset
178 parser = argparse.ArgumentParser()
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parents:
diff changeset
179 parser.add_argument(
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180 'input',
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181 help='input filename with geographical coordinates (netCDF format)'
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182 )
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183
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184 parser.add_argument(
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185 '--proj',
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186 help='Specify the projection on which we draw'
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187 )
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188 parser.add_argument(
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189 'varname',
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190 help='Specify which variable to plot (case sensitive)'
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191 )
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192 parser.add_argument(
2
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193 "--logscale",
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194 help='Plot the log scaled data'
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195 )
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196 parser.add_argument(
0
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197 '--cmap',
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198 help='Specify which colormap to use for plotting'
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199 )
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200 parser.add_argument(
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201 '--output',
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202 help='output filename to store resulting image (png format)'
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203 )
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204 parser.add_argument(
1
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205 '--time',
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206 help='list of times to plot for multiple plots'
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207 )
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208 parser.add_argument(
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209 '--format',
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210 help='format for date/time (default is Month d, yyyy)'
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211 )
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212 parser.add_argument(
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213 '--title',
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214 help='plot title'
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215 )
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216 parser.add_argument(
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217 '--ncol',
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218 help='number of columns for multiple plots'
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219 )
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220 parser.add_argument(
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221 '--nrow',
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222 help='number of rows for multiple plots'
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223 )
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224 parser.add_argument(
0
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225 "-v", "--verbose",
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226 help="switch on verbose mode",
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227 action="store_true")
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228 args = parser.parse_args()
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229
1
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230 if args.time is None:
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231 time = []
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232 else:
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233 time = list(map(int, args.time.split(",")))
2
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234
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235 if args.logscale == 'no':
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236 logscale = False
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237 else:
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238 logscale = True
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239
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240 psymap_plot(args.input, args.proj, args.varname, logscale, args.cmap,
1
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241 args.output, args.verbose, time,
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242 args.nrow, args.ncol, args.format, args.title)