comparison xarray_mapplot.py @ 4:9bbaab36a5d4 draft

"planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit 2166974df82f97557b082a9e55135098e61640c4"

3:663268794710

#                               [--xlim "x1,x2"]
#                               [--ylim "y1,y2"]
#                               [--range "valmin,valmax"]
#                               [--threshold VAL]
#                               [--label label-colorbar]
#                               [--shift]
#                               [-v]
#                               input varname
#
# positional arguments:

#  --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 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)

    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':

    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"

        "-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:

4:9bbaab36a5d4

#                               [--xlim "x1,x2"]
#                               [--ylim "y1,y2"]
#                               [--range "valmin,valmax"]
#                               [--threshold VAL]
#                               [--label label-colorbar]
#                               [--config config-file]
#                               [--shift]
#                               [-v]
#                               input varname
#
# positional arguments:

#  --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
#  --config          plotting parameters are passed via a config file
#                    (overwrite other plotting options)
#  --shift           shift longitudes if specified
#  -v, --verbose    switch on verbose mode
#

import argparse

import xarray as xr  # noqa: E402


class MapPlotXr ():
    def __init__(self, input, varname, output, verbose=False,
                 config_file="", proj="", shift=False):

        li = list(input.split(","))
        if len(li) > 1:
            self.input = li
        else:
            self.input = input

        if proj != "" and proj is not None and Path(proj).exists():
            f = open(proj)
            sdict = ''.join(
                f.read().replace("\n", "").split('{')[1].split('}')[0]
                )
            self.proj = '{' + sdict.strip() + '}'
        else:
            self.proj = None
        self.varname = varname
        self.shift = shift
        self.xylim_supported = False
        self.colorbar = True
        if output is None:
            if type(self.input) is list:
                self.output = Path(self.input[0]).stem + '.png'
            else:
                self.output = Path(self.input).stem + '.png'
        else:
            self.output = output
        self.verbose = verbose
        self.label = {}
        self.time = []
        self.xlim = []
        self.ylim = []
        self.range = []
        self.latitude = "latitude"
        self.longitude = "longitude"
        self.land = 0
        self.ocean = 0
        self.coastline = 0
        self.borders = 0
        self.cmap = "coolwarm"
        self.threshold = ""
        self.title = ""

        if config_file != "" and config_file is not None:
            with open(config_file) as f:
                sdict = ''.join(
                    f.read().replace("\n", "").split('{')[1].split('}')[0]
                    )
                tmp = ast.literal_eval('{' + sdict.strip() + '}')
                for key in tmp:
                    if key == 'time':
                        time = tmp[key]
                        self.time = list(map(int, time.split(",")))
                    if key == 'cmap':
                        self.get_cmap(tmp[key])
                    if key == 'latitude':
                        self.latitude = tmp[key]
                    if key == 'longitude':
                        self.longitude = tmp[key]
                    if key == 'land':
                        self.land = float(tmp[key])
                    if key == 'ocean':
                        self.ocean = float(tmp[key])
                    if key == 'coastline':
                        self.coastline = float(tmp[key])
                    if key == 'borders':
                        self.borders = float(tmp[key])
                    if key == 'xlim':
                        xlim = tmp[key]
                        self.xlim = list(map(float, xlim.split(",")))
                    if key == 'ylim':
                        ylim = tmp[key]
                        self.ylim = list(map(float, ylim.split(",")))
                    if key == 'range':
                        range_values = tmp[key]
                        self.range = list(map(float, range_values.split(",")))
                    if key == 'threshold':
                        self.threshold = float(tmp[key])
                    if key == 'label':
                        self.label['label'] = tmp[key]
                    if key == 'title':
                        self.title = tmp[key]

        if type(self.input) is list:
            self.dset = xr.open_mfdataset(self.input, use_cftime=True)
        else:
            self.dset = xr.open_dataset(self.input, use_cftime=True)

        if verbose:
            print("input: ", self.input)
            print("proj: ", self.proj)
            print("varname: ", self.varname)
            print("time: ", self.time)

    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':

    parser = argparse.ArgumentParser()
    parser.add_argument(
        'input',
        help='input filename with geographical coordinates (netCDF format)'
    )
    parser.add_argument(
        '--proj',
        help='Config file with the projection on which we draw'
    )
    parser.add_argument(
        'varname',
        help='Specify which variable to plot (case sensitive)'
    )
    parser.add_argument(
        '--output',
        help='output filename to store resulting image (png format)'
    )
    parser.add_argument(
        '--config',
        help='pass plotting parameters via a config file'
    )
    parser.add_argument(
        '--shift',
        help='shift longitudes if specified',
        action="store_true"

        "-v", "--verbose",
        help="switch on verbose mode",
        action="store_true")
    args = parser.parse_args()

    dset = MapPlotXr(input=args.input, varname=args.varname,
                     output=args.output, verbose=args.verbose,
                     config_file=args.config, proj=args.proj,
                     shift=args.shift)

    if dset.time == []:
        dset.plot()
    else:
        for t in dset.time: