def main():
from warnings import warn
from .pncparse import pncparse
from PseudoNetCDF.core._functions import pncfunc, pncbfunc
from PseudoNetCDF.pncparse import getparser, pncparse
parser = getparser(has_ofile = False, plot_options = False, interactive = True)
parser.add_argument('--funcs', default = __all__, type = lambda x: x.split(','), help='Functions to evaluate split by , (default: %s)' % ','.join(__all__))
import numpy as np
np.seterr(divide = 'ignore', invalid = 'ignore')
ifiles, options = pncparse(has_ofile = False, interactive = True, parser = parser)
if options.variables is None:
options.variables = set(ifiles[0].variables.keys()).difference(options.coordkeys)
console = createconsole(ifiles, options)
warn("Assumes input order is obs model")
ifile1, ifile2 = ifiles
for k in options.funcs:
console.locals[k] = func = eval(k)
console.locals[k+'_f'] = ofile = pncbfunc(func, ifile1, ifile2)
times = ifile1.variables['time']
tstart = times[:].min()
tstop = times[:].max()
dt = tstop - tstart
for vk in options.variables:
if vk in ('time', 'TFLAG'): continue
print('%.2f,%.2f,%.2f,%s,%s,%s,%f' % (tstart, tstop, dt, vk, func.__doc__.strip(), k, ofile.variables[vk].ravel()[0]))
np.seterr(divide = 'warn', invalid = 'warn')
if options.interactive:
console.interact()
pl.sca(ax)
llabels = [l[0].get_label() for l in llines]
pl.legend(llines, llabels, bbox_to_anchor = (.1, 1), loc = 'upper left', bbox_transform = fig.transFigure, ncol = 6)
if edges:
fig.text(0.95, 0.975, title, horizontalalignment = 'right', verticalalignment = "top", fontsize = 16)
else:
fig.text(0.95, 0.025, title, horizontalalignment = 'right', verticalalignment = "bottom", fontsize = 16)
fig.savefig('%s_%s.%s' % (args.outpath, var_name, args.figformat))
pl.close(fig)
return fig
if __name__ == '__main__':
from PseudoNetCDF.pncparse import getparser, pncparse
parser = getparser(has_ofile = True, plot_options = True, interactive = False)
parser.add_argument("--sigma", dest = "sigma", action = "store_true", default = False,
help = "Plot on sigma coordinate instead of pressure")
parser.add_argument("--scale", dest = "scale", type = str, default = 'log',
help = "Defaults to log, but linear and semilog are also options.")
parser.add_argument("--minmax", dest = "minmax", type = str, default = "None,None",
help = "Use values to set range (xmin, xmax); defaults None,None.")
parser.add_argument("--mask-zeros", dest = "maskzeros", action = "store_true", default = False,
help = "Defaults False.")
parser.add_argument("--minmaxq", dest = "minmaxq", type = str, default = '0,100',
help = "Use quartiles to set range (xmin, xmax); defaults 0,100.")
bbox_to_anchor=(.5, 0.025),
loc='lower center')
ticks = np.linspace(0, args.maxpct, 6)[1:]
labels = ['%s%%' % i for i in ticks]
plt.yticks(ticks, labels)
ax.set_rmax(args.maxpct)
ax.set_clip_on(False)
figpath = args.outpath
fig.savefig(figpath)
if args.verbose > 0: print('Saved fig', figpath)
plt.close(fig)
if __name__ == '__main__':
from PseudoNetCDF.pncparse import getparser, pncparse
parser = getparser(has_ofile=True, plot_options=False, interactive=False)
parser.add_argument('--wind-speed',
dest='windspeed',
default='WS',
help='Wind speed variable')
parser.add_argument('--mask-var',
dest='maskvar',
default='WS',
help='Variable from file two for masking')
parser.add_argument('--wind-dir',
dest='winddir',
default='WD',
help='Wind direction variable')
parser.add_argument('--title', default=None, help='Title for wind rose')
parser.add_argument('--binwidth',
dest='binwidth',
po = np.arange(24) + 0.1 + varwidth / 2
for vi, (time, var) in enumerate(zip(times, vars)):
vals = var[:]
if args.squeeze:
vals = vals.squeeze()
vardesc = getattr(var, 'description', None)
varb = ax.plot(time, vals[:], label=vardesc)
# plt.setp(ax.xaxis.get_ticklabels(),rotation = 45)
plt.legend()
figpath = args.outpath + target + '.' + args.figformat
for pc in args.plotcommands:
exec(pc, globals(), locals())
fig.savefig(figpath)
if args.verbose > 0:
print('Saved fig', figpath)
print(figpath)
if __name__ == '__main__':
from PseudoNetCDF.pncparse import getparser, pncparse
parser = getparser(plot_options=True, has_ofile=True)
parser.epilog += """
-----
box.py inobs inmod target [target ...]
inobs - path to obs
inmod - path to mod
target - variable name
"""
ifiles, args = pncparse(plot_options=True, has_ofile=True, parser=parser)
plotts(args)
def parse_and_run():
import os
from argparse import ArgumentParser
from warnings import warn
from permm import mechanism_dict, Mechanism
from permm.analyses import __all__ as all_analyses
all_mechs = '|'.join(list(mechanism_dict.keys()))
all_analyses = '|'.join(all_analyses)
from PseudoNetCDF.pncparse import getparser, pncparse
parser = ArgumentParser(
description=
"permm (Python Environment for Reaction Mechanism Mathematics)")
parser.add_argument("--gui", dest="graphical", \
action="store_true", default=False, \
help="open a graphical user interactive environment")
parser.add_argument("--mechanism", dest="mechanism", \
default="cb05_camx", help="Chemical mechanisms (e.g., a custom path|%s)" % all_mechs)
parser.add_argument("--analysis", dest="analysis", \
default=None, help="Stock analysis to perform (i.e., %s)" % all_analyses)
parser.add_argument("--scripts",
dest="scripts",
action='append',
default=[],
help="Provide scripts to run")
parser.add_argument("-i",
"--interactive",
dest="interactive",
action='store_true',
default=False,
help="Run interactively")
parser.add_argument(
"--input-role",
dest="inrole",
action='append',
default=[],
help=
"Is this a 'merge' file or a 'concentration' file or any other word indicating type?"
)
parser.add_argument("pseudonetcdf", nargs='*')
options = parser.parse_args()
if len(options.pseudonetcdf) > 0:
pncparser = getparser(has_ofile=False, interactive=True)
ifiles, pncoptions = pncparse(has_ofile=False,
interactive=True,
parser=pncparser,
args=args.pseudonetcdf)
else:
ifiles = []
pncoptions = {}
from permm import netcdf
from permm.Shell import load_environ
try:
mech = mechanism_dict[options.mechanism]
except KeyError:
mech = Mechanism(options.mechanism)
start_script = 0
options.inrole += ['merge'] * (len(ifiles) - len(options.inrole))
for r, ifile in zip(options.inrole, ifiles):
if r == 'merge':
mech.set_mrg(ifile)
else:
vardict = dict([(k, v) for k, v in list(ifile.variables.items())
if k in mech.species_dict])
mech.set_process(r, vardict)
from permm.Shell import PERMConsole
console = PERMConsole()
load_environ(mech, console.locals)
for script in options.scripts:
if os.path.isfile(script):
exec(compile(open(script).read(), script, 'exec'), globals(),
console.locals)
else:
exec(script, globals(), console.locals)
if options.graphical:
console.runsource("from permm.GUI import StartGUI")
console.runsource("StartGUI(mech)")
if options.analysis is not None:
if len(args) < 1:
parser.error(
msg=
"Requires a pyPA mrg file as an argument for analysis output. You can enter an interactive environment (-i), but will not have access to \"netted\" reactions"
)
if options.analysis == "net_balance":
console.runsource(
"from permm.analyses.net_balance import net_balance")
console.runsource("net_balance('%s', '%s', '%s')" %
(options.mechanism, args[0], options.output))
elif options.analysis == "history":
console.runsource("from permm.analyses.history import matrix")
console.runsource(
"history = matrix(mech, [C2O3], [HC+Radical-OH-HO2-O1D], [])")
console.runsource("history.run()")
else:
raise "Unkown analysis"
if options.interactive:
load_environ(mech, console.locals)
console.interact()
