Mercurial > repos > climate > psy_maps
changeset 1:706666d912d5 draft default tip
"planemo upload for repository https://github.com/NordicESMhub/galaxy-tools/tree/master/tools/psy-maps commit 4803d769c7b0b37fa80c69bd7327f6789cd3c6bf"
| author | climate |
|---|---|
| date | Sat, 05 Oct 2019 17:11:18 -0400 |
| parents | db8d76da4174 |
| children | |
| files | psy-maps.xml psymap_simple.py test-data/TS.f2000.T31T31.control.cam.h0.0014-12.png test-data/TS.f2000.T31T31.control.cam.h0.0014-12_ortho.png |
| diffstat | 4 files changed, 169 insertions(+), 22 deletions(-) [+] |
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--- a/psy-maps.xml Thu Apr 25 18:11:49 2019 -0400 +++ b/psy-maps.xml Sat Oct 05 17:11:18 2019 -0400 @@ -1,23 +1,49 @@ -<tool id="psy_maps" name="map plot" version="1.2.0"> +<tool id="psy_maps" name="map plot" version="1.2.1"> <description>gridded (lat/lon) netCDF data</description> <requirements> <requirement type="package" version="3">python</requirement> + <requirement type="package" version="1.2.1">psyplot</requirement> <requirement type="package" version="1.2.0">psy-maps</requirement> <requirement type="package" version="1.2.0">psy-reg</requirement> - <requirement type="package" version="1.2.2">psyplot-gui</requirement> - <requirement type="package" version="1.4.1">netcdf4</requirement> + <requirement type="package" version="1.4.2">netcdf4</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ + HOME=`pwd` && python3 '$__tool_directory__/psymap_simple.py' '$ifilename' '$variable' --proj '$adv.projection' --cmap '$adv.colormap' --output image.png + #if str($adv.multiple_plot.selector) == 'yes' + --time '$adv.multiple_plot.time' + --format '$adv.multiple_plot.format' + --ncol '$adv.multiple_plot.ncol' + --nrow '$adv.multiple_plot.nrow' + #end if + #if str($adv.multiple_plot.title).strip() + --title '$adv.multiple_plot.title' + #end if ]]></command> <inputs> <param name="ifilename" type="data" format="netcdf" label="input with geographical coordinates (netCDF format)"></param> <param name="variable" type="text" value="TS" label="variable name as given in the netCDF file" /> <section name="adv" title="Advanced Options" expanded="false"> + <conditional name="multiple_plot"> + <param name="selector" type="select" label="multiple times"> + <option value="yes">yes</option> + <option value="no" selected="true">no</option> + </param> + <when value="yes"> + <param name="time" type="text" value="0" label="comma separated list of indexes for fields to plot" /> + <param name="format" type="text" value="%Y-%m-%d %H:%M:%S" label="date and time format" /> + <param name="ncol" type="integer" value="1" min="1" max="4" label="number of columns for subplot grid" /> + <param name="nrow" type="integer" value="1" min="1" max="20" label="number of rows for subplot grid" /> + <param name="title" type="text" value="" label="subplot title (repeated on each subplot)" /> + </when> + <when value="no"> + <param name="title" type="text" value="" label="plot title" /> + </when> + </conditional> <param name="projection" type="select"> <option value="" selected="true">PlateCarree</option> <option value="robin">Robinson</option> @@ -55,6 +81,9 @@ <option value="RdBu">RdBu</option> <option value="RdGy">RdGy</option> <option value="RdPu">RdPu</option> + <option value="RdBu_r">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> @@ -115,16 +144,16 @@ <test> <param name="ifilename" value="TS.f2000.T31T31.control.cam.h0.0014-12.nc" /> <param name="variable" value="TS" /> - <param name="adv.projection" value="" /> - <param name="adv.colormap" value="jet" /> + <param name="projection" value="" /> + <param name="colormap" value="jet" /> <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12.png" compare="sim_size" delta="500"/> </test> <test> <param name="ifilename" value="TS.f2000.T31T31.control.cam.h0.0014-12.nc" /> <param name="variable" value="TS" /> - <param name="adv.projection" value="ortho" /> - <param name="adv.colormap" value="jet" /> - <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12.png" compare="sim_size" delta="500"/> + <param name="projection" value="ortho" /> + <param name="colormap" value="RdBu_r" /> + <output name="ofilename" ftype="png" file="TS.f2000.T31T31.control.cam.h0.0014-12_ortho.png" compare="sim_size" delta="500"/> </test> </tests> <help><![CDATA[ @@ -153,7 +182,8 @@ :: - usage: psymap_simple.py [-h] [--proj PROJ] [--cmap CMAP] [--output OUTPUT] [-v] input varname + usage: psymap_simple.py [-h] [--proj PROJ] [--cmap CMAP] [--output OUTPUT] [--time TIME] + [--format FORMAT] [--title TITLE] [--ncol NCOL] [--nrow NROW] [-v] input varname Positional arguments: @@ -170,6 +200,11 @@ --cmap CMAP Specify which colormap to use for plotting --output OUTPUT output filename to store resulting image (png format) -v, --verbose switch on verbose mode + --time TIME list of times to plot for multiple plots + --format FORMAT format for date/time (default is Month d, yyyy) + --title TITLE plot title + --ncol NCOL number of columns for multiple plots + --nrow NROW number of rows for multiple plots It uses psy-maps, a python package to generate plots. More information about psyplot and psy-maps can be found at https://psyplot.readthedocs.io/projects/psy-maps/en/latest/
--- a/psymap_simple.py Thu Apr 25 18:11:49 2019 -0400 +++ b/psymap_simple.py Sat Oct 05 17:11:18 2019 -0400 @@ -17,6 +17,11 @@ # --proj PROJ Specify the projection on which we draw # --cmap CMAP Specify which colormap to use for plotting # --output OUTPUT output filename to store resulting image (png format) +# --time TIMES time index from the file for multiple plots ("0 1 2 3") +# --nrow NROW number of rows for multiple plot grid +# --ncol NCOL number of columns for multiple plot grid +# --format date format such as %Y (for year) %B (for month), etc. +# --title plot or subplot title # -v, --verbose switch on verbose mode # @@ -29,16 +34,34 @@ from matplotlib import pyplot # noqa: I202,E402 import psyplot.project as psy # noqa: I202,E402 +from psyplot import rcParams # noqa: I202,E402 class PsyPlot (): - def __init__(self, input, proj, varname, cmap, output, - verbose=False - ): + def __init__(self, input, proj, varname, cmap, output, verbose=False, + time=[], nrow=1, ncol=1, format="%B %e, %Y", + title=""): self.input = input self.proj = proj self.varname = varname self.cmap = cmap + self.time = time + if format is None: + self.format = "" + else: + self.format = format.replace('X', '%') + if title is None: + self.title = "" + else: + self.title = title + if ncol is None: + self.ncol = 1 + else: + self.ncol = int(ncol) + if nrow is None: + self.nrow = 1 + else: + self.nrow = int(nrow) if output is None: self.output = Path(input).stem + '.png' else: @@ -49,37 +72,101 @@ print("proj: ", self.proj) print("varname: ", self.varname) print("cmap: ", self.cmap) + print("time: ", self.time) + print("ncol: ", self.ncol) + print("nrow: ", self.nrow) + print("title: ", self.title) + print("date format: ", self.format) print("output: ", self.output) def plot(self): + if self.title and self.format: + title = self.title + "\n" + self.format + elif not self.title and self.format: + title = self.format + elif self.title and not self.format: + title = self.title + else: + title = '%(long_name)s' + if self.cmap is None and self.proj is None: - print("op1") psy.plot.mapplot(self.input, name=self.varname, + title=title, clabel='{desc}') - elif self.proj is None or self.proj == '': - print("op2") + elif self.proj is None or not self.proj: psy.plot.mapplot(self.input, name=self.varname, + title=title, cmap=self.cmap, clabel='{desc}') - elif self.cmap is None or self.cmap == '': - print("op3") + elif self.cmap is None or not self.cmap: psy.plot.mapplot(self.input, name=self.varname, projection=self.proj, + title=title, clabel='{desc}') else: - print("op4") psy.plot.mapplot(self.input, name=self.varname, cmap=self.cmap, projection=self.proj, + title=title, clabel='{desc}') pyplot.savefig(self.output) + def multiple_plot(self): + if not self.format: + self.format = "%B %e, %Y" -def psymap_plot(input, proj, varname, cmap, output, verbose): + if not self.title: + title = self.format + else: + title = self.title + "\n" + self.format + mpl.rcParams['figure.figsize'] = [20, 8] + mpl.rcParams.update({'font.size': 8}) + rcParams.update({'plotter.maps.grid_labelsize': 8.0}) + if self.cmap is None and self.proj is None: + m = psy.plot.mapplot(self.input, name=self.varname, + title=title, + ax=(self.nrow, self.ncol), + time=self.time, sort=['time'], + clabel='{desc}') + m.share(keys='bounds') + elif self.proj is None or not self.proj: + m = psy.plot.mapplot(self.input, name=self.varname, + title=title, + ax=(self.nrow, self.ncol), + time=self.time, sort=['time'], + cmap=self.cmap, clabel='{desc}') + m.share(keys='bounds') + elif self.cmap is None or not self.cmap: + m = psy.plot.mapplot(self.input, name=self.varname, + projection=self.proj, + ax=(self.nrow, self.ncol), + time=self.time, sort=['time'], + title=title, + clabel='{desc}') + m.share(keys='bounds') + else: + m = psy.plot.mapplot(self.input, name=self.varname, + cmap=self.cmap, + projection=self.proj, + ax=(self.nrow, self.ncol), + time=self.time, sort=['time'], + title=title, + clabel='{desc}') + m.share(keys='bounds') + + pyplot.savefig(self.output) + + +def psymap_plot(input, proj, varname, cmap, output, verbose, time, + nrow, ncol, format, title): """Generate plot from input filename""" - p = PsyPlot(input, proj, varname, cmap, output, verbose) - p.plot() + p = PsyPlot(input, proj, varname, cmap, output, verbose, time, + nrow, ncol, format, title) + if len(time) == 0: + p.plot() + else: + p.multiple_plot() if __name__ == '__main__': @@ -107,10 +194,35 @@ help='output filename to store resulting image (png format)' ) parser.add_argument( + '--time', + help='list of times to plot for multiple plots' + ) + parser.add_argument( + '--format', + help='format for date/time (default is Month d, yyyy)' + ) + parser.add_argument( + '--title', + help='plot title' + ) + parser.add_argument( + '--ncol', + help='number of columns for multiple plots' + ) + parser.add_argument( + '--nrow', + help='number of rows for multiple plots' + ) + parser.add_argument( "-v", "--verbose", help="switch on verbose mode", action="store_true") args = parser.parse_args() + if args.time is None: + time = [] + else: + time = list(map(int, args.time.split(","))) psymap_plot(args.input, args.proj, args.varname, args.cmap, - args.output, args.verbose) + args.output, args.verbose, time, + args.nrow, args.ncol, args.format, args.title)