def __repr__(self):
from PseudoNetCDF.pncdump import pncdump
from io import StringIO
out = StringIO()
pncdump(self, header=True, outfile=out)
out.seek(0, 0)
return out.read()
def __repr__(self):
from PseudoNetCDF.pncdump import pncdump
import sys
if sys.version_info.major == 3:
from io import StringIO
else:
from StringIO import StringIO
out = StringIO()
pncdump(self, header = True, outfile = out)
out.seek(0, 0)
return out.read()
"""
Parameters
----------
ioapifile : file with IOAPI metadata
"""
nsteps = len(ioapifile.dimensions['TSTEP'])
try:
nrows = len(ioapifile.dimensions['ROW'])
ncols = len(ioapifile.dimensions['COL'])
except Exception:
nrows = ioapifile.NROWS
ncols = ioapifile.NCOLS
# interp to ioapi vglvls
out = self.interpSigma(vglvls=ioapifile.VGLVLS, vgtop=ioapifile.VGTOP)
# repeat to grid
out = out.toPerim(ncols, nrows, nsteps)
for pk in ioapifile.ncattrs():
if pk in ('VAR-LIST', 'FILEDESC', 'HISTORY'):
continue
setattr(out, pk, getattr(ioapifile, pk))
out.updatemeta()
return out
if __name__ == '__main__':
po = bcon_profile('testdata/profile.dat')
from PseudoNetCDF.pncdump import pncdump
pncdump(po)
print(po.variables['ATOL1J'].shape)
print(po.variables['ATOL1J'].dimensions)
def __init__(self, ncffile, options):
master = self.root = Tk()
self.ncffile = ncffile
self.options = options
self.plotted_variables = set()
frame = Frame(master)
frame.grid(row = 0)
codeframe = Frame(master)
codeframe.grid(row = 1)
metaframe = Frame(master)
metaframe.grid(row = 2)
goframe = Frame(frame)
goframe.grid(column = 3, row = 1)
var_label = Label(frame, text = 'Select Variable')
var_label.grid(column = 0, row = 0)
var_scrollbar = Scrollbar(frame, orient = VERTICAL)
var_scrollbar.grid(column = 1, row = 1, sticky = N + S)
self.var = Listbox(frame, selectmode = EXTENDED, exportselection = 0, yscrollcommand = var_scrollbar.set)
self.var.grid(column = 0, row = 1)
var_scrollbar.config(command = self.var.yview)
what_to_do = Label(frame, text = 'Execute')
what_to_do.grid(column = 2, row = 0)
self.method_list = Listbox(frame, selectmode = SINGLE, exportselection = 0)
self.method_list.grid(column = 2, row = 1)
self.pre_txt = StringVar()
pre_label = Label(codeframe, text = 'Before any figures, execute code')
self.pre_txt.set(_pre_code)
pre_label.grid(row = 2, sticky = 'W')
self.pre = Entry(codeframe, width = 120, textvariable = self.pre_txt)
self.pre.grid(row =3, sticky = 'E')
self.before_txt = StringVar()
self.before_txt.set(_before_code)
before_label = Label(codeframe, text = 'Before each figure, execute code')
before_label.grid(row = 4, sticky = 'W')
self.before = Entry(codeframe, width = 120, textvariable = self.before_txt)
self.before.grid(row =5, sticky = 'E')
self.after_txt = StringVar()
self.after_txt.set(_after_code)
after_label = Label(codeframe, text = 'After each figure, execute code')
after_label.grid(row = 6, sticky = 'W')
self.after = Entry(codeframe, width = 120, textvariable = self.after_txt)
self.after.grid(row =7, sticky = 'E')
self.post_txt = StringVar()
self.post_txt.set(_post_code)
post_label = Label(codeframe, text = 'After all figures, execute code')
post_label.grid(row = 8, sticky = 'W')
self.post = Entry(codeframe, width = 120, textvariable = self.post_txt)
self.post.grid(row = 9, sticky = 'E')
options_label = Label(goframe, text = 'Options:')
options_label.grid(column = 0, row = 1, sticky = 'W')
self.logscale = IntVar()
self.logscale.set(0)
c = Checkbutton(goframe, text = "log-scale?", variable = self.logscale)
c.grid(column = 0, row = 2, sticky = 'W')
self.coastlines = IntVar()
self.coastlines.set(_coastlines_opt)
coastlines = Checkbutton(goframe, text = "coastlines?", variable = self.coastlines, justify = LEFT)
coastlines.grid(column = 0, row = 3, sticky = 'W')
self.countries = IntVar()
self.countries.set(_countries_opt)
countries = Checkbutton(goframe, text = "countries?", variable = self.countries, justify = LEFT)
countries.grid(column = 0, row = 4, sticky = 'W')
self.states = IntVar()
self.states.set(_states_opt)
states = Checkbutton(goframe, text = "states?", variable = self.states, justify = LEFT)
states.grid(column = 0, row = 5, sticky = 'W')
self.counties = IntVar()
self.counties.set(_counties_opt)
counties = Checkbutton(goframe, text = "counties?", variable = self.counties, justify = LEFT)
counties.grid(column = 0, row = 6, sticky = 'W')
self.execute_button = Button(goframe, text = "Make Figure", command = self.execute)
self.execute_button.grid(row = 0, column = 0, sticky = 'W')
self.methods = ['mapplot', 'presslat', 'presslon', 'time-lat', 'profile', 'timeseries', 'pressx', 'tileplot', 'plot']
method_labels= ['lat-lon', 'press-lat', 'press-lon', 'time-lat', 'Vertical Profile', 'Time Series', 'press-? (2-D)', 'Tile Plot (2-D)', 'Plot (1-D)']
for method in method_labels:
self.method_list.insert(END, method)
var_keys = [k for k, v in self.ncffile.variables.items() if k not in ('time', 'latitude', 'longitude', 'latitude_bounds', 'longitude_bounds', 'time_bounds', 'tau0', 'tau1', 'TFLAG')]
var_keys.sort()
self.vars = []
for spc in var_keys:
self.var.insert(END, spc)
self.vars.append(spc)
meta_label = Label(metaframe, text = 'Common Data Language Header:')
meta_label.grid(column = 0, row = 0, sticky = 'W')
meta_scrollbar = Scrollbar(metaframe, orient = VERTICAL)
meta_scrollbar.grid(column = 1, row = 1, sticky = N + S)
self.meta = Text(metaframe, height=10, width=118, bg='white', relief='flat', yscrollcommand = meta_scrollbar.set)
self.meta.grid(column = 0, row = 1, sticky = 'W')
from PseudoNetCDF.pncdump import pncdump
try:
from StringIO import StringIO
except ImportError:
from io import StringIO
pdump = StringIO("")
try:
name = ', '.join(options.ifile)
except:
name = 'ifile'
pncdump(self.ncffile, header = True, outfile = pdump, )
pdump.seek(0, 0)
self.meta.insert(END, pdump.read())
self.meta.config(state=DISABLED)
help = Button(goframe, text = 'Help', command = self.help)
help.grid(column = 0, row = 7)
quit = Button(goframe, text = 'Quit', command = self.quit)
quit.grid(column = 0, row = 8)
master.mainloop()
shape = outf.createVariable("SHAPE", "i", ("TSTEP", "LAY", "ROW", "COL"))
shape.__dict__.update(dict(units = "ON/OFF", var_desc = "SHAPE".ljust(16), long_name = "SHAPE".ljust(16)))
shape[:] = 1
irr = outf.createVariable("IRR", "f", ("TSTEP", "RXN"))
irr.__dict__.update(dict(units = pr_tmp.units, var_desc = "IRR".ljust(16), long_name = "IRR".ljust(16)))
ipr = outf.createVariable("IPR", "f", ("TSTEP", "SPECIES", "PROCESS"))
irr.__dict__.update(dict(units = pr_tmp.units, var_desc = "IPR".ljust(16), long_name = "IPR".ljust(16)))
for rr, var in zip(rr_keys,irr.swapaxes(0,1)):
var[:] = irrf.variables[rr][:][idx]
for prc, prcvar in zip(prcs,ipr.swapaxes(0,2)):
for spc, spcvar in zip(spcs,prcvar):
try:
spcvar[:] = iprf.variables['_'.join([prc,spc])][:][idx]
except KeyError as es:
warn(str(es))
return outf
if __name__ == '__main__':
from PseudoNetCDF.pncdump import pncdump
from PseudoNetCDF.cmaqfiles.pa import mrgidx
import sys
x = ', '.join(sys.argv[1:])
try:
pncdump(eval('mrgidx(%s)' % (x,)), name = mrgidx)
except:
print("\nUsage: python -m PseudoNetCDF.cmaqfiles.pa \"ipr_paths, irr_paths, idx\"\n ipr_paths - a single string or list of strings\n irr_paths - a single string or list of strings\n idx - 4D numpy slice indexes a time series\n\n\nExample:\n $ python -m PseudoNetCDF.cmaqfiles.pa \"['CMAQ_IPR1.nc','CMAQ_IPR2.nc'], 'CMAQ_IRR.nc', (slice(None),0,1,1)\"", file = sys.stderr)
def __init__(self, ncffile, options):
try:
from Tkinter import Checkbutton, Frame, Label, Scrollbar
from Tkinter import Listbox, Button, IntVar, Tk, VERTICAL
from Tkinter import EXTENDED, END, N, S, SINGLE, Entry
from Tkinter import StringVar, Text, DISABLED, LEFT
except Exception:
try:
from tkinter import Checkbutton, Frame, Label, Scrollbar
from tkinter import Listbox, Button, IntVar, Tk, VERTICAL
from tkinter import EXTENDED, END, N, S, SINGLE, Entry
from tkinter import StringVar, Text, DISABLED, LEFT
except Exception:
warn('tkinter unavailable')
master = self.root = Tk()
self.ncffile = ncffile
self.options = options
self.plotted_variables = set()
frame = Frame(master)
frame.grid(row=0)
codeframe = Frame(master)
codeframe.grid(row=1)
metaframe = Frame(master)
metaframe.grid(row=2)
goframe = Frame(frame)
goframe.grid(column=3, row=1)
var_label = Label(frame, text='Select Variable')
var_label.grid(column=0, row=0)
var_scrollbar = Scrollbar(frame, orient=VERTICAL)
var_scrollbar.grid(column=1, row=1, sticky=N + S)
self.var = Listbox(frame, selectmode=EXTENDED,
exportselection=0,
yscrollcommand=var_scrollbar.set)
self.var.grid(column=0, row=1)
var_scrollbar.config(command=self.var.yview)
what_to_do = Label(frame, text='Execute')
what_to_do.grid(column=2, row=0)
self.method_list = Listbox(frame, selectmode=SINGLE, exportselection=0)
self.method_list.grid(column=2, row=1)
self.pre_txt = StringVar()
pre_label = Label(codeframe, text='Before any figures, execute code')
self.pre_txt.set(_pre_code)
pre_label.grid(row=2, sticky='W')
self.pre = Entry(codeframe, width=120, textvariable=self.pre_txt)
self.pre.grid(row=3, sticky='E')
self.before_txt = StringVar()
self.before_txt.set(_before_code)
before_label = Label(
codeframe, text='Before each figure, execute code')
before_label.grid(row=4, sticky='W')
self.before = Entry(codeframe, width=120, textvariable=self.before_txt)
self.before.grid(row=5, sticky='E')
self.after_txt = StringVar()
self.after_txt.set(_after_code)
after_label = Label(codeframe, text='After each figure, execute code')
after_label.grid(row=6, sticky='W')
self.after = Entry(codeframe, width=120, textvariable=self.after_txt)
self.after.grid(row=7, sticky='E')
self.post_txt = StringVar()
self.post_txt.set(_post_code)
post_label = Label(codeframe, text='After all figures, execute code')
post_label.grid(row=8, sticky='W')
self.post = Entry(codeframe, width=120, textvariable=self.post_txt)
self.post.grid(row=9, sticky='E')
options_label = Label(goframe, text='Options:')
options_label.grid(column=0, row=1, sticky='W')
self.logscale = IntVar()
self.logscale.set(0)
c = Checkbutton(goframe, text="log-scale?", variable=self.logscale)
c.grid(column=0, row=2, sticky='W')
self.coastlines = IntVar()
self.coastlines.set(_coastlines_opt)
coastlines = Checkbutton(
goframe, text="coastlines?", variable=self.coastlines,
justify=LEFT)
coastlines.grid(column=0, row=3, sticky='W')
self.countries = IntVar()
self.countries.set(_countries_opt)
countries = Checkbutton(
goframe, text="countries?", variable=self.countries, justify=LEFT)
countries.grid(column=0, row=4, sticky='W')
self.states = IntVar()
self.states.set(_states_opt)
states = Checkbutton(goframe, text="states?",
variable=self.states, justify=LEFT)
states.grid(column=0, row=5, sticky='W')
self.counties = IntVar()
self.counties.set(_counties_opt)
counties = Checkbutton(goframe, text="counties?",
variable=self.counties, justify=LEFT)
counties.grid(column=0, row=6, sticky='W')
self.execute_button = Button(
goframe, text="Make Figure", command=self.execute)
self.execute_button.grid(row=0, column=0, sticky='W')
self.methods = ['mapplot', 'presslat', 'presslon', 'time-lat',
'profile', 'timeseries', 'pressx', 'tileplot', 'plot']
method_labels = ['lat-lon', 'press-lat', 'press-lon', 'time-lat',
'Vertical Profile', 'Time Series', 'press-? (2-D)',
'Tile Plot (2-D)', 'Plot (1-D)']
for method in method_labels:
self.method_list.insert(END, method)
var_keys = [k for k, v in self.ncffile.variables.items()
if k not in _coordkeys]
var_keys.sort()
self.vars = []
for spc in var_keys:
self.var.insert(END, spc)
self.vars.append(spc)
meta_label = Label(metaframe, text='Common Data Language Header:')
meta_label.grid(column=0, row=0, sticky='W')
meta_scrollbar = Scrollbar(metaframe, orient=VERTICAL)
meta_scrollbar.grid(column=1, row=1, sticky=N + S)
self.meta = Text(metaframe, height=10, width=118, bg='white',
relief='flat', yscrollcommand=meta_scrollbar.set)
self.meta.grid(column=0, row=1, sticky='W')
from PseudoNetCDF.pncdump import pncdump
try:
from StringIO import StringIO
except ImportError:
from io import StringIO
pdump = StringIO("")
pncdump(self.ncffile, header=True, outfile=pdump, )
pdump.seek(0, 0)
self.meta.insert(END, pdump.read())
self.meta.config(state=DISABLED)
help = Button(goframe, text='Help', command=self.help)
help.grid(column=0, row=7)
quit = Button(goframe, text='Quit', command=self.quit)
quit.grid(column=0, row=8)
master.mainloop()
ks = keys[1:]
self.VGLVLS = self.variables["sigma"]
self.VGTOP = 5000
for k in ks:
try:
assert (np.char.strip(data[k]["name"]) == profile_spcs).all()
assert data[k].dtype == data_type
assert data[k].dtype == data_type
except AssertionError:
raise IOError("File is corrupt or inconsistent")
for w, s, e, n in zip(data["west"], data["south"], data["east"], data["north"]):
assert w[0] == s[0] and e[0] == n[0] and n[0] == s[0]
self.createVariable(
w[0].strip(),
"f",
("sigma-mid", "south_east_north_west"),
units="None",
values=np.array(map(lambda x: tuple(x)[1:], [s, e, n, w])).T,
long_name=w[0].ljust(16),
var_desc=w[0].ljust(16),
)
if __name__ == "__main__":
po = profile("testdata/profile.dat")
from PseudoNetCDF.pncdump import pncdump
pncdump(po)
print(po.variables["ATOL1J"].shape)
print(po.variables["ATOL1J"].dimensions)
irr.__dict__.update(
dict(units=pr_tmp.units,
var_desc="IPR".ljust(16),
long_name="IPR".ljust(16)))
for rr, var in zip(rr_keys, irr.swapaxes(0, 1)):
var[:] = irrf.variables[rr][:][idx]
for prc, prcvar in zip(prcs, ipr.swapaxes(0, 2)):
for spc, spcvar in zip(spcs, prcvar):
try:
spcvar[:] = iprf.variables['_'.join([prc, spc])][:][idx]
except KeyError as es:
warn(str(es))
return outf
if __name__ == '__main__':
from PseudoNetCDF.pncdump import pncdump
from PseudoNetCDF.cmaqfiles.pa import mrgidx
import sys
x = ', '.join(sys.argv[1:])
try:
pncdump(eval('mrgidx(%s)' % (x, )), name=mrgidx)
except:
print(
"\nUsage: python -m PseudoNetCDF.cmaqfiles.pa \"ipr_paths, irr_paths, idx\"\n ipr_paths - a single string or list of strings\n irr_paths - a single string or list of strings\n idx - 4D numpy slice indexes a time series\n\n\nExample:\n $ python -m PseudoNetCDF.cmaqfiles.pa \"['CMAQ_IPR1.nc','CMAQ_IPR2.nc'], 'CMAQ_IRR.nc', (slice(None),0,1,1)\"",
file=sys.stderr)
var.units = 'degrees E'
lon = var[:] = np.arange(blon, elon + lonstep, lonstep)
var = outfile.createVariable('longitude_bounds', 'f', ('longitude', 'nv'))
var.units = 'degrees E'
var[:, 0] = lon - lonstep / 2.
var[:, 1] = lon + lonstep / 2.
var = outfile.createVariable('ozone',
'f', ('latitude', 'longitude'),
missing_value=999)
var.units = 'matm-cm'
var.long_name = var.var_desc = 'ozone'.ljust(16)
var[:] = np.ma.masked_values(
np.array([i for i in datablock], dtype='S1').view('S3').astype('i'),
var.missing_value).reshape(nlats, nlons)
return outfile
class tomsl3(PseudoNetCDFFile):
def __init__(self, path):
cdtoms(path, self)
if __name__ == '__main__':
from PseudoNetCDF.pncdump import pncdump
pfile = cdtoms('test.txt')
pncdump(pfile)
print(pfile.variables['ozone'][2, 3])
datalines[i] = line[1:-1]
else:
data, lat = line.split('lat =')
datalines[i] = data[1:-1].rstrip() + '\n'
lats.append(lat.strip())
n = 3
datalines = ''.join(datalines).split('\n')
var = outfile.createVariable('ozone', 'f', ('LAT', 'LON'))
var.units = 'matm-cm'
var.long_name = var.var_desc = 'ozone'.ljust(16)
var[:] = array([[eval(s[n*i:n*i+n]) for i in range(len(s)/n)] for s in datalines if s.strip() != ''], 'f')
var = outfile.createVariable('lat', 'f', ('LAT',))
var.units = 'degrees N'
var[:] = arange(blat, elat+outfile.latbinsize, outfile.latbinsize)
var = outfile.createVariable('lon', 'f', ('LON',))
var.units = 'degrees E'
var[:] = arange(blon, elon+outfile.lonbinsize, outfile.lonbinsize)
return outfile
if __name__ == '__main__':
from PseudoNetCDF.pncdump import pncdump
pfile = cdtoms('test.txt')
pncdump(pfile)
print(pfile.variables['ozone'][2,3])