| Next changeset 1:c6f2435d680b (2020-04-14) |
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Commit message:
"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/climate-stripes commit aa08ea46712c1cfbaac2e6fcd07c93097751cad3" |
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added:
climate-stripes.xml climate_stripes.py test-data/T2Mclimatology.txt test-data/T2Mstripes.png test-data/T2Mstripes_with_axis.png |
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| diff -r 000000000000 -r fec3147b0206 climate-stripes.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/climate-stripes.xml Sat Oct 05 17:03:08 2019 -0400 |
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| b'@@ -0,0 +1,162 @@\n+<tool id="climate_stripes" name="climate stripes" version="1.0.0">\n+ <description>from timeseries</description>\n+ <requirements>\n+ <requirement type="package" version="3">python</requirement>\n+ <requirement type="package" version="3.1.1">matplotlib</requirement>\n+ <requirement type="package" version="0.25.1">pandas</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ python3 \'$__tool_directory__/climate_stripes.py\'\n+ \'$ifilename\' \'$variable\'\n+ --cmap \'$adv.colormap\'\n+ #if str($title).strip()\n+ --title \'$title\'\n+ #end if\n+ #if str($adv.xname).strip()\n+ --xname \'$adv.xname\'\n+ #end if\n+ #if str($adv.format_date).strip()\n+ --format_date \'$adv.format_date\'\n+ #end if\n+ #if str($adv.format_plot).strip()\n+ --format_plot \'$adv.format_plot\'\n+ #end if\n+ --output image.png\n+ ]]></command>\n+ <inputs>\n+ <param name="ifilename" type="data" format="tabular" label="timeseries to plot"></param>\n+ <param name="variable" type="text" value="global" label="column name to use for plotting" />\n+ <param name="title" type="text" value="" label="plot title" />\n+ <section name="adv" title="Advanced Options" expanded="false">\n+ <param name="xname" type="text" value="" label="column name to use for x-axis" />\n+ <param name="format_date" type="text" value="" label="format for input date/time column" />\n+ <param name="format_plot" type="text" value="" label="format for plotting dates on the x-axis" />\n+ <param name="colormap" type="select">\n+ <option value="Accent">Accent</option>\n+ <option value="Blues">Blues</option>\n+ <option value="BrBG">BrBG</option>\n+ <option value="BuGn">BuGn</option>\n+ <option value="BuPu">BuPu</option>\n+ <option value="CMRmap">CMRmap</option>\n+ <option value="Dark2">Dark2</option>\n+ <option value="GnBu">GnBu</option>\n+ <option value="Greens">Greens</option>\n+ <option value="Greys">Greys</option>\n+ <option value="OrRd">OrRd</option>\n+ <option value="Oranges">Oranges</option>\n+ <option value="PRGn">PRGn</option>\n+ <option value="Paired">Paired</option>\n+ <option value="Pastel1">Pastel1</option>\n+ <option value="Pastel2">Pastel2</option>\n+ <option value="PiYG">PiYG</option>\n+ <option value="PuBu">PuBu</option>\n+ <option value="PuBuGn">PuBuGn</option>\n+ <option value="PuOr">PuOr</option>\n+ <option value="PuRd">PuRd</option>\n+ <option value="Purples">Purples</option>\n+ <option value="RdBu">RdBu</option>\n+ <option value="RdGy">RdGy</option>\n+ <option value="RdPu">RdPu</option>\n+ <option value="RdBu_r" selected="true">RdBu_r</option>\n+ <option value="RdGy_r">RdGy_r</option>\n+ <option value="RdPu_r">RdPu_r</option>\n+ <option value="RdYlBu">RdYlBu</option>\n+ <option value="RdYlGn">RdYlGn</option>\n+ <option value="Reds">Reds</option>\n+ <option value="Set1">Set1</option>\n+ <option value="Set2">Set2</option>\n+ <option value="Set3">Set3</option>\n+ <option value="Spectral">Spectral</option>\n+ <option value="Wistia">Wistia</option>\n+ <option value="YlGn">YlGn</option>\n+ <option value="YlGnBu">YlGnBu</option>\n+ <option value="YlOrBr">YlOrBr</option>\n+ <option value="YlOrRd">YlOrRd</option>\n+ <option value='..b'>\n+ <option value="bone">bone</option>\n+ <option value="brg">brg</option>\n+ <option value="bwr">bwr</option>\n+ <option value="cool">cool</option>\n+ <option value="coolwarm">coolwarm</option>\n+ <option value="copper">copper</option>\n+ <option value="cubehelix">cubehelix</option>\n+ <option value="flag">flag</option>\n+ <option value="gist_earth">gist_earth</option>\n+ <option value="gist_gray">gist_gray</option>\n+ <option value="gist_heat">gist_heat</option>\n+ <option value="gist_ncar">gist_ncar</option>\n+ <option value="gist_rainbow">gist_rainbow</option>\n+ <option value="gist_stern">gist_stern</option>\n+ <option value="gist_yarg">gist_yarg</option>\n+ <option value="gnuplot">gnuplot</option>\n+ <option value="gnuplot2">gnuplot2</option>\n+ <option value="gray">gray</option>\n+ <option value="hot">hot</option>\n+ <option value="hsv">hsv</option>\n+ <option value="jet">jet</option>\n+ <option value="nipy_spectral">nipy_spectral</option>\n+ <option value="ocean">ocean</option>\n+ <option value="pink">pink</option>\n+ <option value="prism">prism</option>\n+ <option value="rainbow">rainbow</option>\n+ <option value="seismic">seismic</option>\n+ <option value="spring">spring</option>\n+ <option value="summer">summer</option>\n+ <option value="tab10">tab10</option>\n+ <option value="tab20">tab20</option>\n+ <option value="tab20b">tab20b</option>\n+ <option value="tab20c">tab20c</option>\n+ <option value="terrain">terrain</option>\n+ <option value="winter">winter</option>\n+ </param>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="ofilename" format="png" from_work_dir="image.png"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="ifilename" value="T2Mclimatology.txt" />\n+ <param name="variable" value="global" />\n+ <output name="ofilename" ftype="png" file="T2Mstripes.png" compare="sim_size" delta="50"/>\n+ </test>\n+ <test>\n+ <param name="ifilename" value="T2Mclimatology.txt" />\n+ <param name="variable" value="global" />\n+ <param name="title" value="Surface Temperature stripes (1979-2019)" />\n+ <param name="colormap" value="OrRd" />\n+ <param name="xname" value="Month" />\n+ <param name="format_date" value="XYXm" />\n+ <param name="format_plot" value="XY" />\n+ <output name="ofilename" ftype="png" file="T2Mstripes_with_axis.png" compare="sim_size" delta="50"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+**Climate stripes**\n+=========================================\n+\n+This tool generate stripes from timeseries and is often used to generate warming stripes.\n+\n+\n+.. class:: infomark\n+\n+ The wrappers aims at creating stripes from a timeseries.\n+ The input file must be in tabular format and must contain at least one column that is used\n+ for creating stripes. By default, no title and no axis are plotted. An additional column\n+ can be specified for date/time and its date and time format must then be specified\n+ with an additional options.\n+\n+**What it does**\n+----------------\n+\n+This tools creates an image (png format) corresponding to the visualization of a timeseries as\n+stripes (see https://www.climate-lab-book.ac.uk/2018/warming-stripes/).\n+By default, the colormap is ``RdBu_r`` and no axis nor title are plotted. These settings can be\n+changed in *Advanced settings*.\n+ ]]></help>\n+ <citations>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r fec3147b0206 climate_stripes.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/climate_stripes.py Sat Oct 05 17:03:08 2019 -0400 |
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| @@ -0,0 +1,152 @@ +#!/usr/bin/env python3 +# +# +# usage: climate_stripes.py [-h] [--cmap CMAP] +# [--output OUTPUT] +# [--xname XNAME] +# [--format_plot FORMAT_PLOT] +# [--format_date FORMAT_DATE] +# [--title TITLE] +# [--nxsplit NXSPLIT] +# input varname +# +# positional arguments: +# input input filename with timeseries (tabular format) +# varname column name to use for plotting (case sensitive) +# +# optional arguments: +# -h, --help show this help message and exit +# --cmap CMAP Specify which colormap to use for plotting +# --output OUTPUT output filename to store resulting image (png format) +# --xname XNAME column name to use for x-axis +# --format_plot FORMAT_PLOT +# format for plotting dates on the x-axis +# --format_date FORMAT_DATE +# format for input date/time column +# --title TITLE plot title +# --nxsplit NXSPLIT number of ticks on the x-axis +# + +import argparse +import warnings + +import matplotlib as mpl +mpl.use('Agg') + +import matplotlib.pyplot as plt # noqa: I202,E402 + +import numpy as np # noqa: I202,E402 + +import pandas as pd # noqa: I202,E402 + + +class Stripes (): + def __init__(self, input, valname, cmap, output, xname="", + date_format='%Y%m', + plot_format='%Y', + nxsplit=10, + title=""): + self.input = input + self.valname = valname + self.xname = xname + if not nxsplit: + self.nxsplit = 10 + else: + self.nxsplit = nxsplit + if not cmap: + self.cmap = 'RdBu_r' + else: + self.cmap = cmap + if not output: + self.output = "stripes.png" + else: + self.output = output + self.title = title + if not date_format: + self.format = '%Y%m' + else: + self.format = date_format.replace('X', '%') + if not plot_format: + self.plot_format = self.format + else: + self.plot_format = plot_format.replace('X', '%') + + def read_data(self): + self.data = pd.read_csv(self.input, sep='\t') + + def create_stripes(self): + data = np.zeros((2, self.data[self.valname].shape[0]), dtype='float') + data[:] = np.NaN + data[0, :] = self.data[self.valname] + data[1, :] = self.data[self.valname] + fig = plt.figure(figsize=(10, 2)) + ax = plt.subplot(111) + plt.pcolor(data, cmap=self.cmap, + vmin=self.data[self.valname].min(), + vmax=self.data[self.valname].max()) + if self.title: + plt.title(self.title) + if self.xname: + nrange = self.data.index.values + n = int(np.floor((nrange.max() - nrange.min())/int(self.nxsplit))) + date_list = self.data[self.xname].loc[::n].apply( + lambda x: pd.to_datetime(str(x), + format=self.format)) + date_list = [i.strftime(self.plot_format) for i in date_list] + nval = int(self.data[self.xname].loc[::n].shape[0]) + ax.xaxis.set_major_locator(plt.MaxNLocator(nval)) + ax.xaxis.set_ticklabels(date_list) + ax.xaxis.set_tick_params(rotation=45) + else: + ax.set_xticks([]) + ax.set_yticks([]) + fig.tight_layout() + fig.savefig(self.output) + + +if __name__ == '__main__': + warnings.filterwarnings("ignore") + parser = argparse.ArgumentParser() + parser.add_argument( + 'input', + help='input filename with geographical coordinates (netCDF format)' + ) + parser.add_argument( + 'varname', + help='column name to use for plotting (case sensitive)' + ) + parser.add_argument( + '--cmap', + help='Specify which colormap to use for plotting' + ) + parser.add_argument( + '--output', + help='output filename to store resulting image (png format)' + ) + parser.add_argument( + '--xname', + help='column name to use for x-axis' + ) + parser.add_argument( + '--format_plot', + help='format for plotting dates on the x-axis' + ) + parser.add_argument( + '--format_date', + help='format for input date/time column (default is Month d, yyyy)' + ) + parser.add_argument( + '--title', + help='plot title' + ) + parser.add_argument( + '--nxsplit', + help='number of ticks on the x-axis' + ) + args = parser.parse_args() + stripes = Stripes(args.input, args.varname, args.cmap, args.output, + xname=args.xname, date_format=args.format_date, + plot_format=args.format_plot, title=args.title, + nxsplit=args.nxsplit) + stripes.read_data() + stripes.create_stripes() |
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| diff -r 000000000000 -r fec3147b0206 test-data/T2Mclimatology.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/T2Mclimatology.txt Sat Oct 05 17:03:08 2019 -0400 |
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| @@ -0,0 +1,489 @@ +Month global +197901 -0.2309 +197902 -0.4906 +197903 -0.2922 +197904 -0.3259 +197905 -0.2858 +197906 -0.258 +197907 -0.3306 +197908 -0.2336 +197909 -0.1801 +197910 -0.1248 +197911 -0.147 +197912 0.0667 +198001 -0.1084 +198002 -0.0513 +198003 -0.0826 +198004 -0.0015 +198005 0.0697 +198006 -0.0799 +198007 -0.0425 +198008 -0.1085 +198009 -0.1715 +198010 -0.216 +198011 -0.192 +198012 -0.2736 +198101 0.0171 +198102 -0.0524 +198103 0.0305 +198104 -0.0305 +198105 -0.069 +198106 -0.0755 +198107 -0.0747 +198108 -0.0603 +198109 -0.1398 +198110 -0.1792 +198111 -0.1878 +198112 -0.0359 +198201 -0.3861 +198202 -0.2909 +198203 -0.4431 +198204 -0.3551 +198205 -0.2111 +198206 -0.2463 +198207 -0.1711 +198208 -0.2779 +198209 -0.2693 +198210 -0.2803 +198211 -0.2834 +198212 -0.0342 +198301 0.0396 +198302 0.004 +198303 0.006 +198304 -0.0941 +198305 0.0277 +198306 -0.092 +198307 -0.1496 +198308 -0.0738 +198309 -0.0007 +198310 -0.2356 +198311 -0.1167 +198312 -0.2251 +198401 -0.2111 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