Mercurial > repos > ecology > timeseries_extraction
view xarray_netcdf2netcdf.py @ 0:810820a0d45c draft default tip
planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
author | ecology |
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date | Sun, 31 Jul 2022 21:23:21 +0000 |
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#!/usr/bin/env python3 # # Apply operations on selected variables # - scale # one can also select the range of time (for timeseries) # to apply these operations over the range only # when a range of time is selected and when scaling, one # can choose to save the entire timeseries or # the selected range only. # when scaling, one can add additional filters on dimensions # (typically used to filter over latitudes and longitudes) import argparse import re import warnings from pathlib import Path import xarray as xr # noqa: E402 class netCDF2netCDF (): def __init__(self, infile, varname, scale="", output="output.netcdf", write_all=False, keep_attributes=True, filter_list="", where_config="", other="", sel=False, drop=False, verbose=False): self.drop = drop if Path(where_config).exists(): f = open(where_config) self.where = f.read().replace("\n", "") else: self.where = "" self.other = other self.sel = sel li = list(infile.split(",")) if len(li) > 1: self.infile = li else: self.infile = infile self.verbose = verbose if varname == 'None' or varname is None: self.varname = varname else: li = list(varname.split(",")) self.varname = li self.write_all = write_all self.keep_attributes = keep_attributes if self.keep_attributes: xr.set_options(keep_attrs=True) self.filter = filter_list self.selection = {} self.method = {} if scale == "" or scale is None: self.scale = 1 else: self.scale = float(scale) if output is None: self.output = "output.netcdf" else: self.output = output # initialization self.dset = None self.subset = None if self.verbose: print("infile: ", self.infile) print("varname: ", self.varname) print("filter_list: ", self.filter) print("scale: ", self.scale) print("write_all: ", self.write_all) print("keep_attributes: ", self.keep_attributes) print("sel: ", self.sel) print("output: ", self.output) def apply_selection(self): self.dset = self.ds for key in self.selection: if 'slice' in str(self.selection[key]): self.dset = self.dset.sel( {key: self.selection[key]} ) else: self.dset = self.dset.sel( {key: self.selection[key]}, method=self.method[key] ) def dimension_selection(self, single_filter): split_filter = single_filter.split('#') dimension_varname = split_filter[0] op = split_filter[1] if self.sel: ll = float(split_filter[2]) else: ll = int(split_filter[2]) if (op == 'sl'): if self.sel: rl = float(split_filter[3]) else: rl = int(split_filter[3]) self.selection[dimension_varname] = slice(ll, rl) elif (op == 'to'): self.selection[dimension_varname] = slice(None, ll) elif (op == 'from'): self.selection[dimension_varname] = slice(ll, None) elif (op == 'is'): self.selection[dimension_varname] = ll if self.sel: rl = split_filter[3] if 'None' in rl: self.method[dimension_varname] = None else: self.method[dimension_varname] = rl def filter_selection(self): for single_filter in self.filter: self.dimension_selection(single_filter) if self.sel: self.apply_selection() else: self.dset = \ self.ds.isel(self.selection) if self.varname != 'None' and self.varname is not None: for var in self.varname: self.dset[var] = \ self.dset[var]*self.scale def compute(self): if self.dset is None: if type(self.infile) is list: self.ds = xr.open_mfdataset(self.infile) else: self.ds = xr.open_dataset(self.infile) if self.where != "": if self.drop: if self.verbose: print("Where with drop=True") self.ds = self.ds.where( self.eval_where(self.where), drop=True ) elif self.other is not None and self.other != "": if self.verbose: print("Where with other=", float(self.other)) self.ds = self.ds.where( self.eval_where(self.where), other=float(self.other) ) else: self.ds = self.ds.where( self.eval_where(self.where) ) self.filter_selection() if self.verbose: print(self.selection) def save(self): if self.varname != 'None' and \ self.varname is not None and \ not self.write_all: self.dset[self.varname].to_netcdf(self.output) else: self.dset.to_netcdf(self.output) def is_float(self, element) -> bool: try: float(element) return True except ValueError: return False def eval_where(self, where_condition): eval_cond = None list_names = list(set( list(self.ds.keys()) + list(self.ds.coords.keys())) ) wcond = where_condition check_cond = where_condition for var in list_names: wcond = wcond.replace(var, ' self.ds.' + var + ' ') check_cond = check_cond.replace(var, '') to_remove = "[><=&|()]" check_cond = re.sub(to_remove, "", check_cond).replace("!", "") check_cond = re.sub(' +', ' ', check_cond).strip() list_flt = check_cond.split(" ") no_convert = False for num in list_flt: if not self.is_float(num): no_convert = True if not no_convert: eval_cond = eval(wcond) return eval_cond if __name__ == '__main__': warnings.filterwarnings("ignore") parser = argparse.ArgumentParser() parser.add_argument( 'input', help='input filename in netCDF format' ) parser.add_argument( 'varname', help='Specify which variable to plot (case sensitive)' ) parser.add_argument( '--filter', nargs="*", help='Filter list variable#operator#value_s#value_e' ) parser.add_argument( '--where', help='filename with where condition to be evaluated' ) parser.add_argument( '--output', help='Output filename to store the resulting netCDF file' ) parser.add_argument( '--scale', help='scale factor to apply to selection (float)' ) parser.add_argument( '--other', help='Value to use for locations where condition is False (float)' ) parser.add_argument( "--write_all", help="write all data to netCDF", action="store_true") parser.add_argument( "--keep_attributes", help="Keep all attributes", action="store_true") parser.add_argument( "-v", "--verbose", help="switch on verbose mode", action="store_true") parser.add_argument( "--selection", help="select by values", action="store_true") parser.add_argument( "--drop", help="drop values where condition is not met", action="store_true") args = parser.parse_args() print("args.selection", args.selection) dset = netCDF2netCDF(infile=args.input, varname=args.varname, scale=args.scale, output=args.output, write_all=args.write_all, sel=args.selection, keep_attributes=args.keep_attributes, filter_list=args.filter, where_config=args.where, drop=args.drop, other=args.other, verbose=args.verbose) dset.compute() dset.save()