Mercurial > repos > climate > climate_stripes
changeset 0:fec3147b0206 draft
"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 |
| files | climate-stripes.xml climate_stripes.py test-data/T2Mclimatology.txt test-data/T2Mstripes.png test-data/T2Mstripes_with_axis.png |
| diffstat | 5 files changed, 803 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/climate-stripes.xml Sat Oct 05 17:03:08 2019 -0400 @@ -0,0 +1,162 @@ +<tool id="climate_stripes" name="climate stripes" version="1.0.0"> + <description>from timeseries</description> + <requirements> + <requirement type="package" version="3">python</requirement> + <requirement type="package" version="3.1.1">matplotlib</requirement> + <requirement type="package" version="0.25.1">pandas</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python3 '$__tool_directory__/climate_stripes.py' + '$ifilename' '$variable' + --cmap '$adv.colormap' + #if str($title).strip() + --title '$title' + #end if + #if str($adv.xname).strip() + --xname '$adv.xname' + #end if + #if str($adv.format_date).strip() + --format_date '$adv.format_date' + #end if + #if str($adv.format_plot).strip() + --format_plot '$adv.format_plot' + #end if + --output image.png + ]]></command> + <inputs> + <param name="ifilename" type="data" format="tabular" label="timeseries to plot"></param> + <param name="variable" type="text" value="global" label="column name to use for plotting" /> + <param name="title" type="text" value="" label="plot title" /> + <section name="adv" title="Advanced Options" expanded="false"> + <param name="xname" type="text" value="" label="column name to use for x-axis" /> + <param name="format_date" type="text" value="" label="format for input date/time column" /> + <param name="format_plot" type="text" value="" label="format for plotting dates on the x-axis" /> + <param name="colormap" type="select"> + <option value="Accent">Accent</option> + <option value="Blues">Blues</option> + <option value="BrBG">BrBG</option> + <option value="BuGn">BuGn</option> + <option value="BuPu">BuPu</option> + <option value="CMRmap">CMRmap</option> + <option value="Dark2">Dark2</option> + <option value="GnBu">GnBu</option> + <option value="Greens">Greens</option> + <option value="Greys">Greys</option> + <option value="OrRd">OrRd</option> + <option value="Oranges">Oranges</option> + <option value="PRGn">PRGn</option> + <option value="Paired">Paired</option> + <option value="Pastel1">Pastel1</option> + <option value="Pastel2">Pastel2</option> + <option value="PiYG">PiYG</option> + <option value="PuBu">PuBu</option> + <option value="PuBuGn">PuBuGn</option> + <option value="PuOr">PuOr</option> + <option value="PuRd">PuRd</option> + <option value="Purples">Purples</option> + <option value="RdBu">RdBu</option> + <option value="RdGy">RdGy</option> + <option value="RdPu">RdPu</option> + <option value="RdBu_r" selected="true">RdBu_r</option> + <option value="RdGy_r">RdGy_r</option> + <option value="RdPu_r">RdPu_r</option> + <option value="RdYlBu">RdYlBu</option> + <option value="RdYlGn">RdYlGn</option> + <option value="Reds">Reds</option> + <option value="Set1">Set1</option> + <option value="Set2">Set2</option> + <option value="Set3">Set3</option> + <option value="Spectral">Spectral</option> + <option value="Wistia">Wistia</option> + <option value="YlGn">YlGn</option> + <option value="YlGnBu">YlGnBu</option> + <option value="YlOrBr">YlOrBr</option> + <option value="YlOrRd">YlOrRd</option> + <option value="afmhot">afmhot</option> + <option value="autumn">autumn</option> + <option value="binary">binary</option> + <option value="bone">bone</option> + <option value="brg">brg</option> + <option value="bwr">bwr</option> + <option value="cool">cool</option> + <option value="coolwarm">coolwarm</option> + <option value="copper">copper</option> + <option value="cubehelix">cubehelix</option> + <option value="flag">flag</option> + <option value="gist_earth">gist_earth</option> + <option value="gist_gray">gist_gray</option> + <option value="gist_heat">gist_heat</option> + <option value="gist_ncar">gist_ncar</option> + <option value="gist_rainbow">gist_rainbow</option> + <option value="gist_stern">gist_stern</option> + <option value="gist_yarg">gist_yarg</option> + <option value="gnuplot">gnuplot</option> + <option value="gnuplot2">gnuplot2</option> + <option value="gray">gray</option> + <option value="hot">hot</option> + <option value="hsv">hsv</option> + <option value="jet">jet</option> + <option value="nipy_spectral">nipy_spectral</option> + <option value="ocean">ocean</option> + <option value="pink">pink</option> + <option value="prism">prism</option> + <option value="rainbow">rainbow</option> + <option value="seismic">seismic</option> + <option value="spring">spring</option> + <option value="summer">summer</option> + <option value="tab10">tab10</option> + <option value="tab20">tab20</option> + <option value="tab20b">tab20b</option> + <option value="tab20c">tab20c</option> + <option value="terrain">terrain</option> + <option value="winter">winter</option> + </param> + </section> + </inputs> + <outputs> + <data name="ofilename" format="png" from_work_dir="image.png"/> + </outputs> + <tests> + <test> + <param name="ifilename" value="T2Mclimatology.txt" /> + <param name="variable" value="global" /> + <output name="ofilename" ftype="png" file="T2Mstripes.png" compare="sim_size" delta="50"/> + </test> + <test> + <param name="ifilename" value="T2Mclimatology.txt" /> + <param name="variable" value="global" /> + <param name="title" value="Surface Temperature stripes (1979-2019)" /> + <param name="colormap" value="OrRd" /> + <param name="xname" value="Month" /> + <param name="format_date" value="XYXm" /> + <param name="format_plot" value="XY" /> + <output name="ofilename" ftype="png" file="T2Mstripes_with_axis.png" compare="sim_size" delta="50"/> + </test> + </tests> + <help><![CDATA[ + +**Climate stripes** +========================================= + +This tool generate stripes from timeseries and is often used to generate warming stripes. + + +.. class:: infomark + + The wrappers aims at creating stripes from a timeseries. + The input file must be in tabular format and must contain at least one column that is used + for creating stripes. By default, no title and no axis are plotted. An additional column + can be specified for date/time and its date and time format must then be specified + with an additional options. + +**What it does** +---------------- + +This tools creates an image (png format) corresponding to the visualization of a timeseries as +stripes (see https://www.climate-lab-book.ac.uk/2018/warming-stripes/). +By default, the colormap is ``RdBu_r`` and no axis nor title are plotted. These settings can be +changed in *Advanced settings*. + ]]></help> + <citations> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/climate_stripes.py Sat Oct 05 17:03:08 2019 -0400 @@ -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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