Mercurial > repos > climate > climate_stripes

comparison climate_stripes.py @ 0:fec3147b0206 draft

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"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes commit aa08ea46712c1cfbaac2e6fcd07c93097751cad3"
author climate
date Sat, 05 Oct 2019 17:03:08 -0400
parents
children c6f2435d680b
comparison
equal deleted inserted replaced
-1:000000000000 0:fec3147b0206
1 #!/usr/bin/env python3
2 #
3 #
4 # usage: climate_stripes.py [-h] [--cmap CMAP]
5 # [--output OUTPUT]
6 # [--xname XNAME]
7 # [--format_plot FORMAT_PLOT]
8 # [--format_date FORMAT_DATE]
9 # [--title TITLE]
10 # [--nxsplit NXSPLIT]
11 # input varname
12 #
13 # positional arguments:
14 # input input filename with timeseries (tabular format)
15 # varname column name to use for plotting (case sensitive)
16 #
17 # optional arguments:
18 # -h, --help show this help message and exit
19 # --cmap CMAP Specify which colormap to use for plotting
20 # --output OUTPUT output filename to store resulting image (png format)
21 # --xname XNAME column name to use for x-axis
22 # --format_plot FORMAT_PLOT
23 # format for plotting dates on the x-axis
24 # --format_date FORMAT_DATE
25 # format for input date/time column
26 # --title TITLE plot title
27 # --nxsplit NXSPLIT number of ticks on the x-axis
28 #
29
30 import argparse
31 import warnings
32
33 import matplotlib as mpl
34 mpl.use('Agg')
35
36 import matplotlib.pyplot as plt # noqa: I202,E402
37
38 import numpy as np # noqa: I202,E402
39
40 import pandas as pd # noqa: I202,E402
41
42
43 class Stripes ():
44 def __init__(self, input, valname, cmap, output, xname="",
45 date_format='%Y%m',
46 plot_format='%Y',
47 nxsplit=10,
48 title=""):
49 self.input = input
50 self.valname = valname
51 self.xname = xname
52 if not nxsplit:
53 self.nxsplit = 10
54 else:
55 self.nxsplit = nxsplit
56 if not cmap:
57 self.cmap = 'RdBu_r'
58 else:
59 self.cmap = cmap
60 if not output:
61 self.output = "stripes.png"
62 else:
63 self.output = output
64 self.title = title
65 if not date_format:
66 self.format = '%Y%m'
67 else:
68 self.format = date_format.replace('X', '%')
69 if not plot_format:
70 self.plot_format = self.format
71 else:
72 self.plot_format = plot_format.replace('X', '%')
73
74 def read_data(self):
75 self.data = pd.read_csv(self.input, sep='\t')
76
77 def create_stripes(self):
78 data = np.zeros((2, self.data[self.valname].shape[0]), dtype='float')
79 data[:] = np.NaN
80 data[0, :] = self.data[self.valname]
81 data[1, :] = self.data[self.valname]
82 fig = plt.figure(figsize=(10, 2))
83 ax = plt.subplot(111)
84 plt.pcolor(data, cmap=self.cmap,
85 vmin=self.data[self.valname].min(),
86 vmax=self.data[self.valname].max())
87 if self.title:
88 plt.title(self.title)
89 if self.xname:
90 nrange = self.data.index.values
91 n = int(np.floor((nrange.max() - nrange.min())/int(self.nxsplit)))
92 date_list = self.data[self.xname].loc[::n].apply(
93 lambda x: pd.to_datetime(str(x),
94 format=self.format))
95 date_list = [i.strftime(self.plot_format) for i in date_list]
96 nval = int(self.data[self.xname].loc[::n].shape[0])
97 ax.xaxis.set_major_locator(plt.MaxNLocator(nval))
98 ax.xaxis.set_ticklabels(date_list)
99 ax.xaxis.set_tick_params(rotation=45)
100 else:
101 ax.set_xticks([])
102 ax.set_yticks([])
103 fig.tight_layout()
104 fig.savefig(self.output)
105
106
107 if __name__ == '__main__':
108 warnings.filterwarnings("ignore")
109 parser = argparse.ArgumentParser()
110 parser.add_argument(
111 'input',
112 help='input filename with geographical coordinates (netCDF format)'
113 )
114 parser.add_argument(
115 'varname',
116 help='column name to use for plotting (case sensitive)'
117 )
118 parser.add_argument(
119 '--cmap',
120 help='Specify which colormap to use for plotting'
121 )
122 parser.add_argument(
123 '--output',
124 help='output filename to store resulting image (png format)'
125 )
126 parser.add_argument(
127 '--xname',
128 help='column name to use for x-axis'
129 )
130 parser.add_argument(
131 '--format_plot',
132 help='format for plotting dates on the x-axis'
133 )
134 parser.add_argument(
135 '--format_date',
136 help='format for input date/time column (default is Month d, yyyy)'
137 )
138 parser.add_argument(
139 '--title',
140 help='plot title'
141 )
142 parser.add_argument(
143 '--nxsplit',
144 help='number of ticks on the x-axis'
145 )
146 args = parser.parse_args()
147 stripes = Stripes(args.input, args.varname, args.cmap, args.output,
148 xname=args.xname, date_format=args.format_date,
149 plot_format=args.format_plot, title=args.title,
150 nxsplit=args.nxsplit)
151 stripes.read_data()
152 stripes.create_stripes()