diff xarray_mapplot.py @ 0:fea8a53f8099 draft

"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 57b6d23e3734d883e71081c78e77964d61be82ba"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/xarray_mapplot.py	Sun Jun 06 08:50:43 2021 +0000
@@ -0,0 +1,457 @@
+#!/usr/bin/env python3
+#
+#
+# usage: xarray_mapplot.py [-h] [--proj PROJ]
+#                               [--cmap CMAP]
+#                               [--output OUTPUT]
+#                               [--time TIMES]
+#                               [--nrow NROW]
+#                               [--ncol NCOL]
+#                               [--title title]
+#                               [--latitude LATITUDE]
+#                               [--longitude LONGITUDE]
+#                               [--land ALPHA-LAND]
+#                               [--ocean ALPHA-OCEAN]
+#                               [--coastline ALPHA-COASTLINE]
+#                               [--borders ALPHA-BORDERS]
+#                               [--xlim "x1,x2"]
+#                               [--ylim "y1,y2"]
+#                               [--range "valmin,valmax"]
+#                               [--threshold VAL]
+#                               [--label label-colorbar]
+#                               [--shift]
+#                               [-v]
+#                               input varname
+#
+# positional arguments:
+#  input            input filename with geographical coordinates (netCDF
+#                   format)
+#  varname          Specify which variable to plot (case sensitive)
+#
+# optional arguments:
+#  -h, --help       show this help message and exit
+#  --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")
+#  --title          plot or subplot title
+#  --latitude        variable name for latitude
+#  --longitude       variable name for longitude
+#  --land            add land on plot with alpha value [0-1]
+#  --ocean           add oceans on plot with alpha value [0-1]
+#  --coastline       add coastline with alpha value [0-1]
+#  --borders         add country borders with alpha value [0-1]
+#  --xlim            limited geographical area longitudes "x1,x2"
+#  --ylim            limited geographical area latitudes "y1,y2"
+#  --range           "valmin,valmax" for plotting
+#  --threshold       do not plot values below threshold
+#  --label           set a label for colormap
+#  --shift           shift longitudes if specified
+#  -v, --verbose    switch on verbose mode
+#
+
+import argparse
+import ast
+import warnings
+from pathlib import Path
+
+import cartopy.crs as ccrs
+import cartopy.feature as feature
+
+from cmcrameri import cm
+
+import matplotlib as mpl
+mpl.use('Agg')
+from matplotlib import pyplot  # noqa: I202,E402
+
+import xarray as xr  # noqa: E402
+
+
+class MapPlotXr ():
+    def __init__(self, input, proj, varname, cmap, output, verbose=False,
+                 time=[], title="", latitude="latitude",
+                 longitude="longitude", land=0, ocean=0,
+                 coastline=0, borders=0, xlim=[], ylim=[],
+                 threshold="", label="", shift=False,
+                 range_values=[]):
+        self.input = input
+        print("PROJ", proj)
+        if proj != "" and proj is not None:
+            self.proj = proj.replace('X', ':')
+        else:
+            self.proj = proj
+        self.varname = varname
+        self.get_cmap(cmap)
+        self.time = time
+        self.latitude = latitude
+        self.longitude = longitude
+        self.land = land
+        self.ocean = ocean
+        self.coastline = coastline
+        self.borders = borders
+        self.xlim = xlim
+        self.ylim = ylim
+        self.range = range_values
+        self.threshold = threshold
+        self.shift = shift
+        self.xylim_supported = False
+        self.colorbar = True
+        self.title = title
+        if output is None:
+            self.output = Path(input).stem + '.png'
+        else:
+            self.output = output
+        self.verbose = verbose
+        self.dset = xr.open_dataset(self.input, use_cftime=True)
+
+        self.label = {}
+        if label != "" and label is not None:
+            self.label['label'] = label
+        if verbose:
+            print("input: ", self.input)
+            print("proj: ", self.proj)
+            print("varname: ", self.varname)
+            print("time: ", self.time)
+            print("minval, maxval: ", self.range)
+            print("title: ", self.title)
+            print("output: ", self.output)
+            print("label: ", self.label)
+            print("shift: ", self.shift)
+            print("ocean: ", self.ocean)
+            print("land: ", self.land)
+            print("coastline: ", self.coastline)
+            print("borders: ", self.borders)
+            print("latitude: ", self.latitude)
+            print("longitude: ", self.longitude)
+            print("xlim: ", self.xlim)
+            print("ylim: ", self.ylim)
+
+    def get_cmap(self, cmap):
+        if cmap[0:3] == 'cm.':
+            self.cmap = cm.__dict__[cmap[3:]]
+        else:
+            self.cmap = cmap
+
+    def projection(self):
+        if self.proj is None:
+            return ccrs.PlateCarree()
+
+        proj_dict = ast.literal_eval(self.proj)
+
+        user_proj = proj_dict.pop("proj")
+        if user_proj == 'PlateCarree':
+            self.xylim_supported = True
+            return ccrs.PlateCarree(**proj_dict)
+        elif user_proj == 'AlbersEqualArea':
+            return ccrs.AlbersEqualArea(**proj_dict)
+        elif user_proj == 'AzimuthalEquidistant':
+            return ccrs.AzimuthalEquidistant(**proj_dict)
+        elif user_proj == 'EquidistantConic':
+            return ccrs.EquidistantConic(**proj_dict)
+        elif user_proj == 'LambertConformal':
+            return ccrs.LambertConformal(**proj_dict)
+        elif user_proj == 'LambertCylindrical':
+            return ccrs.LambertCylindrical(**proj_dict)
+        elif user_proj == 'Mercator':
+            return ccrs.Mercator(**proj_dict)
+        elif user_proj == 'Miller':
+            return ccrs.Miller(**proj_dict)
+        elif user_proj == 'Mollweide':
+            return ccrs.Mollweide(**proj_dict)
+        elif user_proj == 'Orthographic':
+            return ccrs.Orthographic(**proj_dict)
+        elif user_proj == 'Robinson':
+            return ccrs.Robinson(**proj_dict)
+        elif user_proj == 'Sinusoidal':
+            return ccrs.Sinusoidal(**proj_dict)
+        elif user_proj == 'Stereographic':
+            return ccrs.Stereographic(**proj_dict)
+        elif user_proj == 'TransverseMercator':
+            return ccrs.TransverseMercator(**proj_dict)
+        elif user_proj == 'UTM':
+            return ccrs.UTM(**proj_dict)
+        elif user_proj == 'InterruptedGoodeHomolosine':
+            return ccrs.InterruptedGoodeHomolosine(**proj_dict)
+        elif user_proj == 'RotatedPole':
+            return ccrs.RotatedPole(**proj_dict)
+        elif user_proj == 'OSGB':
+            self.xylim_supported = False
+            return ccrs.OSGB(**proj_dict)
+        elif user_proj == 'EuroPP':
+            self.xylim_supported = False
+            return ccrs.EuroPP(**proj_dict)
+        elif user_proj == 'Geostationary':
+            return ccrs.Geostationary(**proj_dict)
+        elif user_proj == 'NearsidePerspective':
+            return ccrs.NearsidePerspective(**proj_dict)
+        elif user_proj == 'EckertI':
+            return ccrs.EckertI(**proj_dict)
+        elif user_proj == 'EckertII':
+            return ccrs.EckertII(**proj_dict)
+        elif user_proj == 'EckertIII':
+            return ccrs.EckertIII(**proj_dict)
+        elif user_proj == 'EckertIV':
+            return ccrs.EckertIV(**proj_dict)
+        elif user_proj == 'EckertV':
+            return ccrs.EckertV(**proj_dict)
+        elif user_proj == 'EckertVI':
+            return ccrs.EckertVI(**proj_dict)
+        elif user_proj == 'EqualEarth':
+            return ccrs.EqualEarth(**proj_dict)
+        elif user_proj == 'Gnomonic':
+            return ccrs.Gnomonic(**proj_dict)
+        elif user_proj == 'LambertAzimuthalEqualArea':
+            return ccrs.LambertAzimuthalEqualArea(**proj_dict)
+        elif user_proj == 'NorthPolarStereo':
+            return ccrs.NorthPolarStereo(**proj_dict)
+        elif user_proj == 'OSNI':
+            return ccrs.OSNI(**proj_dict)
+        elif user_proj == 'SouthPolarStereo':
+            return ccrs.SouthPolarStereo(**proj_dict)
+
+    def plot(self, ts=None):
+        if self.shift:
+            if self.longitude == 'longitude':
+                self.dset = self.dset.assign_coords(
+                                 longitude=(((
+                                        self.dset[self.longitude]
+                                        + 180) % 360) - 180))
+            elif self.longitude == 'lon':
+                self.dset = self.dset.assign_coords(
+                                 lon=(((self.dset[self.longitude]
+                                        + 180) % 360) - 180))
+
+        pyplot.figure(1, figsize=[20, 10])
+
+        # Set the projection to use for plotting
+        ax = pyplot.subplot(1, 1, 1, projection=self.projection())
+        if self.land:
+            ax.add_feature(feature.LAND, alpha=self.land)
+
+        if self.ocean:
+            ax.add_feature(feature.OCEAN, alpha=self.ocean)
+        if self.coastline:
+            ax.coastlines(resolution='10m', alpha=self.coastline)
+        if self.borders:
+            ax.add_feature(feature.BORDERS, linestyle=':', alpha=self.borders)
+
+        if self.xlim:
+            min_lon = min(self.xlim[0], self.xlim[1])
+            max_lon = max(self.xlim[0], self.xlim[1])
+        else:
+            min_lon = self.dset[self.longitude].min()
+            max_lon = self.dset[self.longitude].max()
+
+        if self.ylim:
+            min_lat = min(self.ylim[0], self.ylim[1])
+            max_lat = max(self.ylim[0], self.ylim[1])
+        else:
+            min_lat = self.dset[self.latitude].min()
+            max_lat = self.dset[self.latitude].max()
+
+        if self.xylim_supported:
+            pyplot.xlim(min_lon, max_lon)
+            pyplot.ylim(min_lat, max_lat)
+
+        # Fix extent
+        if self.threshold == "" or self.threshold is None:
+            threshold = self.dset[self.varname].min()
+        else:
+            threshold = float(self.threshold)
+
+        if self.range == []:
+            minval = self.dset[self.varname].min()
+            maxval = self.dset[self.varname].max()
+        else:
+            minval = self.range[0]
+            maxval = self.range[1]
+
+        if self.verbose:
+            print("minval: ", minval)
+            print("maxval: ", maxval)
+
+        # pass extent with vmin and vmax parameters
+        proj_t = ccrs.PlateCarree()
+        if ts is None:
+            self.dset.where(
+                 self.dset[self.varname] > threshold
+                 )[self.varname].plot(ax=ax,
+                                      vmin=minval,
+                                      vmax=maxval,
+                                      transform=proj_t,
+                                      cmap=self.cmap,
+                                      cbar_kwargs=self.label
+                                      )
+            if self.title != "" and self.title is not None:
+                pyplot.title(self.title)
+            pyplot.savefig(self.output)
+        else:
+            if self.colorbar:
+                self.dset.where(
+                     self.dset[self.varname] > threshold
+                     )[self.varname].isel(time=ts).plot(ax=ax,
+                                                        vmin=minval,
+                                                        vmax=maxval,
+                                                        transform=proj_t,
+                                                        cmap=self.cmap,
+                                                        cbar_kwargs=self.label
+                                                        )
+            else:
+                self.dset.where(
+                     self.dset[self.varname] > minval
+                     )[self.varname].isel(time=ts).plot(ax=ax,
+                                                        vmin=minval,
+                                                        vmax=maxval,
+                                                        transform=proj_t,
+                                                        cmap=self.cmap,
+                                                        add_colorbar=False)
+            if self.title != "" and self.title is not None:
+                pyplot.title(self.title + "(time = " + str(ts) + ')')
+            pyplot.savefig(self.output[:-4] + "_time" + str(ts) +
+                           self.output[-4:])  # assume png format
+
+
+if __name__ == '__main__':
+    warnings.filterwarnings("ignore")
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        'input',
+        help='input filename with geographical coordinates (netCDF format)'
+    )
+
+    parser.add_argument(
+        '--proj',
+        help='Specify the projection on which we draw'
+    )
+    parser.add_argument(
+        'varname',
+        help='Specify which variable to plot (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(
+        '--time',
+        help='list of times to plot for multiple plots'
+    )
+    parser.add_argument(
+        '--title',
+        help='plot title'
+    )
+    parser.add_argument(
+        '--latitude',
+        help='variable name for latitude'
+    )
+    parser.add_argument(
+        '--longitude',
+        help='variable name for longitude'
+    )
+    parser.add_argument(
+        '--land',
+        help='add land on plot with alpha value [0-1]'
+    )
+    parser.add_argument(
+        '--ocean',
+        help='add oceans on plot with alpha value [0-1]'
+    )
+    parser.add_argument(
+        '--coastline',
+        help='add coastline with alpha value [0-1]'
+    )
+    parser.add_argument(
+        '--borders',
+        help='add country borders with alpha value [0-1]'
+    )
+    parser.add_argument(
+        '--xlim',
+        help='limited geographical area longitudes "x1,x2"'
+    )
+    parser.add_argument(
+        '--ylim',
+        help='limited geographical area latitudes "y1,y2"'
+    )
+    parser.add_argument(
+        '--range',
+        help='min and max values for plotting "minval,maxval"'
+    )
+    parser.add_argument(
+        '--threshold',
+        help='do not plot values below threshold'
+    )
+    parser.add_argument(
+        '--label',
+        help='set a label for colorbar'
+    )
+    parser.add_argument(
+        '--shift',
+        help='shift longitudes if specified',
+        action="store_true"
+    )
+    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(",")))
+    if args.xlim is None:
+        xlim = []
+    else:
+        xlim = list(map(float, args.xlim.split(",")))
+    if args.ylim is None:
+        ylim = []
+    else:
+        ylim = list(map(float, args.ylim.split(",")))
+    if args.range is None:
+        range_values = []
+    else:
+        range_values = list(map(float, args.range.split(",")))
+    if args.latitude is None:
+        latitude = "latitude"
+    else:
+        latitude = args.latitude
+    if args.longitude is None:
+        longitude = "longitude"
+    else:
+        longitude = args.longitude
+    if args.land is None:
+        land = 0
+    else:
+        land = float(args.land)
+    if args.ocean is None:
+        ocean = 0
+    else:
+        ocean = float(args.ocean)
+    if args.coastline is None:
+        coastline = 0
+    else:
+        coastline = float(args.coastline)
+    if args.borders is None:
+        borders = 0
+    else:
+        borders = float(args.borders)
+
+    dset = MapPlotXr(input=args.input, proj=args.proj, varname=args.varname,
+                     cmap=args.cmap, output=args.output, verbose=args.verbose,
+                     time=time, title=args.title,
+                     latitude=latitude, longitude=longitude, land=land,
+                     ocean=ocean, coastline=coastline, borders=borders,
+                     xlim=xlim, ylim=ylim, threshold=args.threshold,
+                     label=args.label, shift=args.shift,
+                     range_values=range_values)
+
+    if dset.time == []:
+        dset.plot()
+    else:
+        for t in dset.time:
+            dset.plot(t)
+            dset.shift = False   # only shift once
+            dset.colorbar = True