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import os
import netCDF4
import csv
import re
import textwrap
from datetime import datetime
from numpy import any as numpy_any
from numpy import arange as numpy_arange
from numpy import arccos as numpy_arccos
from numpy import arcsin as numpy_arcsin
from numpy import array as numpy_array
from numpy import clip as numpy_clip
from numpy import column_stack as numpy_column_stack
from numpy import cos as numpy_cos
from numpy import deg2rad as numpy_deg2rad
from numpy import dtype as numpy_dtype
from numpy import empty as numpy_empty
from numpy import mean as numpy_mean
from numpy import pi as numpy_pi
from numpy import rad2deg as numpy_rad2deg
from numpy import resize as numpy_resize
from numpy import result_type as numpy_result_type
from numpy import sin as numpy_sin
from numpy import transpose as numpy_transpose
from numpy import where as numpy_where
from netCDF4 import date2num as netCDF4_date2num
from .. import __version__, __Conventions__, __file__
from ..domain import Domain
from ..coordinatereference import CoordinateReference
from ..field import Field, FieldList
from ..cellmethods import CellMethods
from ..cfdatetime import Datetime
from ..coordinate import DimensionCoordinate, AuxiliaryCoordinate
from ..functions import RTOL, ATOL, equals
from ..units import Units
from ..functions import (open_files_threshold_exceeded, close_one_file,
abspath)
from ..data.data import Data, Partition, PartitionMatrix
from .filearray import UMFileArray
from .functions import _open_um_file
from .umread.umfile import UMFileException
# --------------------------------------------------------------------
# Constants
# --------------------------------------------------------------------
_pi_over_180 = numpy_pi/180.0
# PP missing data indicator
_pp_rmdi = -1.0e+30
# Reference surface pressure in Pascals
_pstar = 1.0e5
# --------------------------------------------------------------------
# Characters used in decoding LBEXP into a runid
# --------------------------------------------------------------------
_characters = ('a','b','c','d','e','f','g','h','i','j','k','l','m',
'n','o','p','q','r','s','t','u','v','w','x','y','z',
'0','1','2','3','4','5','6','7','8','9')
_n_characters = len(_characters)
# --------------------------------------------------------------------
# Number matching regular expression
# --------------------------------------------------------------------
_number_regex = '([-+]?\d*\.?\d+(e[-+]?\d+)?)'
# --------------------------------------------------------------------
# Date-time object that copes with non-standard calendars
# --------------------------------------------------------------------
netCDF4_netcdftime_datetime = netCDF4.netcdftime.datetime
# --------------------------------------------------------------------
# Caches for derived values
# --------------------------------------------------------------------
_cache_latlon = {}
_cached_runid = {}
_cached_latlon = {}
_cached_time = {}
_cached_ctime = {}
_cached_size_1_height_coordinate = {}
_cached_z_coordinate = {}
_cached_date2num = {}
_cached_model_level_number_coordinate = {}
_Units = {
None : Units(),
'' : Units(''),
'1' : Units('1'),
'Pa' : Units('Pa'),
'm' : Units('m'),
'hPa' : Units('hPa'),
'K' : Units('K'),
'degrees' : Units('degrees'),
'degrees_east' : Units('degrees_east'),
'degrees_north' : Units('degrees_north'),
'days' : Units('days'),
'gregorian 1752-9-13': Units('days since 1752-9-13', 'gregorian'),
'365_day 1752-9-13' : Units('days since 1752-9-13', '365_day'),
'360_day 0-1-1' : Units('days since 0-1-1', '360_day'),
}
# --------------------------------------------------------------------
# Names of PP integer and real header items
# --------------------------------------------------------------------
_header_names = ('LBYR', 'LBMON', 'LBDAT', 'LBHR', 'LBMIN', 'LBDAY',
'LBYRD', 'LBMOND', 'LBDATD', 'LBHRD', 'LBMIND',
'LBDAYD', 'LBTIM', 'LBFT', 'LBLREC', 'LBCODE', 'LBHEM',
'LBROW', 'LBNPT', 'LBEXT', 'LBPACK', 'LBREL', 'LBFC',
'LBCFC', 'LBPROC', 'LBVC', 'LBRVC', 'LBEXP', 'LBEGIN',
'LBNREC', 'LBPROJ', 'LBTYP', 'LBLEV', 'LBRSVD1',
'LBRSVD2', 'LBRSVD3', 'LBRSVD4', 'LBSRCE', 'LBUSER1',
'LBUSER2', 'LBUSER3', 'LBUSER4', 'LBUSER5', 'LBUSER6',
'LBUSER7',
'BRSVD1', 'BRSVD2', 'BRSVD3', 'BRSVD4',
'BDATUM', 'BACC', 'BLEV', 'BRLEV', 'BHLEV', 'BHRLEV',
'BPLAT', 'BPLON', 'BGOR',
'BZY', 'BDY', 'BZX', 'BDX', 'BMDI', 'BMKS')
# --------------------------------------------------------------------
# Positions of PP header items in their arrays
# --------------------------------------------------------------------
(lbyr, lbmon, lbdat, lbhr, lbmin, lbday,
lbyrd, lbmond, lbdatd, lbhrd, lbmind,
lbdayd, lbtim, lbft, lblrec, lbcode, lbhem,
lbrow, lbnpt, lbext, lbpack, lbrel, lbfc,
lbcfc, lbproc, lbvc, lbrvc, lbexp, lbegin,
lbnrec, lbproj, lbtyp, lblev, lbrsvd1,
lbrsvd2, lbrsvd3, lbrsvd4, lbsrce, lbuser1,
lbuser2, lbuser3, lbuser4, lbuser5, lbuser6,
lbuser7,
) = range(45)
(brsvd1, brsvd2, brsvd3, brsvd4,
bdatum, bacc, blev, brlev, bhlev, bhrlev,
bplat, bplon, bgor,
bzy, bdy, bzx, bdx, bmdi, bmks,
) = range(19)
# --------------------------------------------------------------------
# Assign CF standard name attributes to PP axis codes. (The full list
# of field code keys may be found at
# http://cms.ncas.ac.uk/html_umdocs/wave/@header.)
# --------------------------------------------------------------------
_coord_standard_name = {
0 : None, # Sigma (or eta, for hybrid coordinate data).
1 : 'air_pressure', # Pressure (mb).
2 : 'altitude', # Height above sea level (km).
3 : 'atmosphere_hybrid_sigma_pressure_coordinate', # Eta (U.M. hybrid coordinates) only.
4 : 'depth', # Depth below sea level (m)
5 : 'model_level_number', # Model level.
6 : 'air_potential_temperature', # Theta
7 : 'atmosphere_sigma_coordinate', # Sigma only.
8 : None, # Sigma-theta
10 : 'latitude', # Latitude (degrees N).
11 : 'longitude', # Longitude (degrees E).
13 : 'region', # Site number (set of parallel rows or columns e.g.Time series)
14 : 'atmosphere_hybrid_height_coordinate',
15 : 'height',
20 : 'time', # Time (days) (Gregorian calendar (not 360 day year))
21 : 'time', # Time (months)
22 : 'time', # Time (years)
23 : 'time', # Time (model days with 360 day model calendar)
40 : None, # pseudolevel
99 : None, # Other
-10 : 'grid_latitude', # Rotated latitude (degrees).
-11 : 'grid_longitude', # Rotated longitude (degrees).
-20 : 'radiation_wavelength',
}
# --------------------------------------------------------------------
# Assign CF long names to PP axis codes.
# --------------------------------------------------------------------
_coord_long_name = {}
# --------------------------------------------------------------------
# Assign CF units strings to PP axis codes.
# --------------------------------------------------------------------
#_coord_units = {
_axiscode_to_units = {
0 : '1', # Sigma (or eta, for hybrid coordinate data)
1 : 'hPa', # air_pressure
2 : 'm', # altitude
3 : '1', # atmosphere_hybrid_sigma_pressure_coordinate
4 : 'm', # depth
5 : '1', # model_level_number
6 : 'K', # air_potential_temperature
7 : '1', # atmosphere_sigma_coordinate
10 : 'degrees_north', # latitude
11 : 'degrees_east', # longitude
13 : '', # region
14 : '1', # atmosphere_hybrid_height_coordinate
15 : 'm', # height
20 : 'days', # time (gregorian)
23 : 'days', # time (360_day)
40 : '1', # pseudolevel
-10 : 'degrees', # rotated latitude (not an official axis code)
-11 : 'degrees', # rotated longitude (not an official axis code)
}
_axiscode_to_Units = {
0 : _Units['1'], # Sigma (or eta, for hybrid coordinate data)
1 : _Units['hPa'], # air_pressure
2 : _Units['m'], # altitude
3 : _Units['1'], # atmosphere_hybrid_sigma_pressure_coordinate
4 : _Units['m'], # depth
5 : _Units['1'], # model_level_number
6 : _Units['K'], # air_potential_temperature
7 : _Units['1'], # atmosphere_sigma_coordinate
10 : _Units['degrees_north'], # latitude
11 : _Units['degrees_east'], # longitude
13 : _Units[''], # region
14 : _Units['1'], # atmosphere_hybrid_height_coordinate
15 : _Units['m'], # height
20 : _Units['days'], # time (gregorian)
23 : _Units['days'], # time (360_day)
40 : _Units['1'], # pseudolevel
-10 : _Units['degrees'], # rotated latitude (not an official axis code)
-11 : _Units['degrees'], # rotated longitude (not an official axis code)
}
# --------------------------------------------------------------------
# Assign CF axis attributes to PP axis codes.
# --------------------------------------------------------------------
_coord_axis = {
1 : 'Z', # air_pressure
2 : 'Z', # altitude
3 : 'Z', # atmosphere_hybrid_sigma_pressure_coordinate
4 : 'Z', # depth
5 : 'Z', # model_level_number
6 : 'Z', # air_potential_temperature
7 : 'Z', # atmosphere_sigma_coordinate
10 : 'Y', # latitude
11 : 'X', # longitude
13 : None, # region
14 : 'Z', # atmosphere_hybrid_height_coordinate
15 : 'Z', # height
20 : 'T', # time (gregorian)
23 : 'T', # time (360_day)
40 : None, # pseudolevel
-10 : 'Y', # rotated latitude (not an official axis code)
-11 : 'X', # rotated longitude (not an official axis code)
}
# --------------------------------------------------------------------
# Assign CF positive attributes to PP axis codes.
# --------------------------------------------------------------------
_coord_positive = {
1 : 'down', # air_pressure
2 : 'up', # altitude
3 : 'down', # atmosphere_hybrid_sigma_pressure_coordinate
4 : 'down', # depth
5 : None, # model_level_number
6 : 'up', # air_potential_temperature
7 : 'down', # atmosphere_sigma_coordinate
10 : None, # latitude
11 : None, # longitude
13 : None, # region
14 : 'up', # atmosphere_hybrid_height_coordinate
15 : 'up', # height
20 : None, # time (gregorian)
23 : None, # time (360_day)
40 : None, # pseudolevel
-10 : None, # rotated latitude (not an official axis code)
-11 : None, # rotated longitude (not an official axis code)
}
# --------------------------------------------------------------------
# Translate LBVC codes to PP axis codes. (The full list of field code
# keys may be found at
# http://cms.ncas.ac.uk/html_umdocs/wave/@fcodes.)
# --------------------------------------------------------------------
_lbvc_to_axiscode = {
1 : 2, # altitude (Height)
2 : 4, # depth (Depth)
3 : None, # (Geopotential (= g*height))
4 : None, # (ICAO height)
6 : 5, # model_level_number
7 : None, # (Exner pressure)
8 : 1, # air_pressure (Pressure)
9 : 3, # atmosphere_hybrid_sigma_pressure_coordinate (Hybrid pressure)
10 : 7, # atmosphere_sigma_coordinate (Sigma (= p/surface p)) ## dch check
16 : None, # (Temperature T)
19 : 6, # air_potential_temperature (Potential temperature)
27 : None, # (Atmospheric) density
28 : None, # (d(p*)/dt . p* = surface pressure)
44 : None, # (Time in seconds)
65 : 14, # atmosphere_hybrid_height_coordinate (Hybrid height)
129 : None, # Surface
176 : 10, # latitude (Latitude)
177 : 11, # longitude (Longitude)
}
# --------------------------------------------------------------------
# Names of PP extra data codes
# --------------------------------------------------------------------
_extra_data_name = {
1 : 'x',
2 : 'y',
3 : 'y_domain_lower_bound',
4 : 'x_domain_lower_bound',
5 : 'y_domain_upper_bound',
6 : 'x_domain_upper_bound',
7 : 'z_domain_lower_bound',
8 : 'x_domain_upper_bound',
9 : 'title',
10 : 'domain_title',
11 : 'x_lower_bound',
12 : 'x_upper_bound',
13 : 'y_lower_bound',
14 : 'y_upper_bound',
}
# --------------------------------------------------------------------
# Model identifier codes. These are the the last four digits of
# LBSRCE.
# --------------------------------------------------------------------
_lbsrce_model_codes = {1111 : 'UM'}
# --------------------------------------------------------------------
# LBCODE values for unrotated latitude longitude grids
# --------------------------------------------------------------------
_true_latitude_longitude_lbcodes = set((1, 2))
# --------------------------------------------------------------------
# LBCODE values for rotated latitude longitude grids
# --------------------------------------------------------------------
_rotated_latitude_longitude_lbcodes = set((101, 102, 111))
_axis = {'t' : 'dim0',
'z' : 'dim1',
'y' : 'dim2',
'x' : 'dim3',
'r' : 'dim4',
'p' : 'dim5',
'area': None,
}
class UMField(object):
'''
'''
_debug = False
def __init__(self, var, fmt, byte_ordering, word_size, um_version,
set_standard_name, height_at_top_of_model, **kwargs):
'''
**Initialization**
:Parameters:
var : cf.um.umread.umfile.Var
byte_ordering : str
'little_endian' or 'big_endian'
word_size : int
Word size in bytes (4 or 8).
fmt : str
'PP' or 'FF'
um_version : number
set_standard_name : bool
If True then set the standard_name CF property.
height_at_top_of_model : float, optional
**kwargs : *optional*
Keyword arguments specifying CF properties for the UM field.
'''
self._nonzero = False
self.fmt = fmt
self.height_at_top_of_model = height_at_top_of_model
self.byte_ordering = byte_ordering
self.word_size = word_size
self.atol = ATOL()
self.domain = Domain()
cf_properties = {}
attributes = {}
self.fields = []
filename = abspath(var.file.path)
self.filename = filename
groups = var.group_records_by_extra_data()
n_groups = len(groups)
if n_groups == 1:
# There is one group of records
groups_nz = [var.nz]
groups_nt = [var.nt]
elif n_groups > 1:
# There are multiple groups of records, distinguished by
# different extra data.
groups_nz = []
groups_nt = []
groups2 = []
for group in groups:
group_size = len(group)
if group_size == 1:
# There is only one record in this group
split_group= False
nz = 1
elif group_size > 1:
# There are multiple records in this group
# Find the lengths of runs of identical times
times = [(self.header_vtime(rec), self.header_dtime(rec))
for rec in group]
lengths = [len(tuple(g)) for k, g in itertools.groupby(times)]
if len(set(lengths)) == 1:
# Each run of identical times has the same
# length, so it is possible that this group
# forms a variable of nz x nt records.
split_group = False
nz = lengths.pop()
z0 = [self.z for rec in group[:nz]]
for i in range(nz, group_size, nz):
z1 = [self.header_z(rec) for rec in group[i:i+nz]]
if z1 != z0:
split_group = True
break
else:
# Different runs of identical times have
# different lengths, so it is not possible for
# this group to form a variable of nz x nt
# records.
split_group = True
nz = 1
#--- End: if
if split_group:
# This group doesn't form a complete nz x nt
# matrix, so split it up into 1 x 1 groups.
groups2.extend([[rec] for rec in group])
groups_nz.extend([1] * group_size)
groups_nt.extend([1] * group_size)
else:
# This group forms a complete nz x nt matrix, so
# it may be considered as a variable in its own
# right and doesn't need to be split up.
groups2.append(group)
groups_nz.append(nz)
groups_nt.append(group_size/nz)
#--- End: for
groups = groups2
#--- End: if
rec0 = groups[0][0]
int_hdr = rec0.int_hdr
self.int_hdr_dtype = int_hdr.dtype
int_hdr = int_hdr.tolist()
real_hdr = rec0.real_hdr.tolist()
self.int_hdr = int_hdr
self.real_hdr = real_hdr
# ------------------------------------------------------------
# Set some metadata quantities which are guaranteed to be the
# same for all records in a variable
# ------------------------------------------------------------
LBNPT = int_hdr[lbnpt]
LBROW = int_hdr[lbrow]
LBTIM = int_hdr[lbtim]
LBCODE = int_hdr[lbcode]
LBPROC = int_hdr[lbproc]
LBVC = int_hdr[lbvc]
LBUSER5 = int_hdr[lbuser5]
BPLAT = real_hdr[bplat]
BPLON = real_hdr[bplon]
BDX = real_hdr[bdx]
BDY = real_hdr[bdy]
self.lbnpt = LBNPT
self.lbrow = LBROW
self.lbtim = LBTIM
self.lbproc = LBPROC
self.lbvc = LBVC
self.bplat = BPLAT
self.bplon = BPLON
self.bdx = BDX
self.bdy = BDY
# ------------------------------------------------------------
# Set some derived metadata quantities which are (as good as)
# guaranteed to be the same for all records in a variable
# ------------------------------------------------------------
self.lbtim_ia, ib = divmod(LBTIM, 100)
self.lbtim_ib, ic = divmod(ib, 10)
if ic == 1:
calendar = 'gregorian'
elif ic == 4:
calendar = '365_day'
else:
calendar = '360_day'
self.calendar = calendar
self.reference_time_Units()
header_um_version, source = divmod(int_hdr[lbsrce], 10000)
if header_um_version > 0 and int(um_version) == um_version: #len(um_version) <= 3:
# header_um_version = str(header_um_version)
model_um_version = header_um_version
self.um_version = header_um_version
else:
model_um_version = None
self.um_version = um_version
# Set source
source = _lbsrce_model_codes.setdefault(source, None)
if source is not None and model_um_version is not None:
source += ' vn%s' % model_um_version
if source:
cf_properties['source'] = source
# ------------------------------------------------------------
# Set the T, Z, Y and X axis codes. These are guaranteed to be
# the same for all records in a variable.
# ------------------------------------------------------------
if LBCODE == 1 or LBCODE == 2:
# 1 = Unrotated regular lat/long grid
# 2 = Regular lat/lon grid boxes (grid points are box
# centres)
ix = 11
iy = 10
elif LBCODE == 101 or LBCODE == 102:
# 101 = Rotated regular lat/long grid
# 102 = Rotated regular lat/lon grid boxes (grid points
# are box centres)
ix = -11 # rotated longitude (not an official axis code)
iy = -10 # rotated latitude (not an official axis code)
elif LBCODE >= 10000:
# Cross section
ix, iy = divmod(divmod(LBCODE, 10000)[1], 100)
else:
ix = None
iy = None
iz = _lbvc_to_axiscode.setdefault(LBVC, None)
# Set it from the calendar type
if iy in (20, 23) or ix in (20, 23):
# Time is dealt with by x or y
it = None
elif calendar == 'gregorian':
it = 20
else:
it = 23
self.ix = ix
self.iy = iy
self.iz = iz
self.it = it
self.cf_info = {}
# Set a identifying name based on the submodel and STASHcode
# (or field code).
stash = int_hdr[lbuser4]
submodel = int_hdr[lbuser7]
self.stash = stash
# The STASH code has been set in the PP header, so try to find
# its standard_name from the conversion table
stash_records = _stash2standard_name.get((submodel, stash), None)
um_Units = None
long_name = None
um_condition = None
if stash_records:
um_version = self.um_version
for (long_name,
units,
valid_from,
valid_to,
standard_name,
cf_info,
um_condition) in stash_records:
# Check that conditions are met
if not self.test_um_version(valid_from, valid_to, um_version):
continue
if um_condition:
if not self.test_um_condition(um_condition,
LBCODE, BPLAT, BPLON):
continue
# Still here? Then we have our standard_name, etc.
if standard_name:
if set_standard_name:
cf_properties['standard_name'] = standard_name
else:
attributes['_standard_name'] = standard_name
cf_properties['long_name'] = long_name.rstrip()
um_Units = _Units.get(units, None)
if um_Units is None:
um_Units = Units(units)
_Units[units] = um_Units
self.um_Units = um_Units
self.cf_info = cf_info
break
#--- End: for
#--- End: if
if stash:
section, item = divmod(stash, 1000)
um_stash_source = 'm%02ds%02di%03d' % (submodel, section, item)
cf_properties['um_stash_source'] = um_stash_source
identity = 'UM_%s_vn%s' % (um_stash_source, self.um_version)
else:
identity = 'UM_%d_fc%d_vn%s' % (submodel, int_hdr[lbfc],
self.um_version)
if um_Units is None:
self.um_Units = _Units[None]
if um_condition:
identity += '_%s' % um_condition
if long_name is None:
cf_properties['long_name'] = identity
for recs, nz, nt in zip(groups, groups_nz, groups_nt):
self.recs = recs
self.nz = nz
self.nt = nt
self.z_recs = recs[:nz]
self.t_recs = recs[::nz]
LBUSER5 = recs[0].int_hdr.item(lbuser5,)
self.cell_method_axis_name = {'area': 'area'}
self.down_axes = set()
self.z_axis = 'z'
# ------------------------------------------------------------
# Get the extra data for this group
# ------------------------------------------------------------
extra = recs[0].get_extra_data()
self.extra = extra
# ------------------------------------------------------------
# Set some derived metadata quantities
# ------------------------------------------------------------
if self._debug:
print self.__dict__
self.printfdr()
# ------------------------------------------------------------
# Create the 'T' dimension coordinate
# ------------------------------------------------------------
axiscode = it
if axiscode is not None:
c = self.time_coordinate(axiscode)
# ------------------------------------------------------------
# Create the 'Z' dimension coordinate
# ------------------------------------------------------------
axiscode = iz
if axiscode is not None:
# Get 'Z' coordinate from LBVC
if axiscode == 3:
c = self.atmosphere_hybrid_sigma_pressure_coordinate(axiscode)
elif axiscode == 2 and 'height' in self.cf_info:
# Create the height coordinate from the information
# given in the STASH to standard_name conversion table
height, units = self.cf_info['height']
c = self.size_1_height_coordinate(axiscode, height, units)
elif axiscode == 14:
c = self.atmosphere_hybrid_height_coordinate(axiscode)
else:
c = self.z_coordinate(axiscode)
# Create a model_level_number auxiliary coordinate
LBLEV = int_hdr[lblev]
if LBVC in (2, 9, 65) or LBLEV in (7777, 8888): # CHECK!
self.LBLEV = LBLEV
c = self.model_level_number_coordinate(aux=bool(c))
#--- End: if
# ------------------------------------------------------------
# Create the 'Y' dimension coordinate
# ------------------------------------------------------------
axiscode = iy
yc = None
if axiscode is not None:
if axiscode in (20, 23):
# 'Y' axis is time-since-reference-date
if extra.get('y', None) is not None:
c = self.time_coordinate_from_extra_data(axiscode, 'y')
else:
LBUSER3 = int_hdr[lbuser3]
if LBUSER3 == LBROW:
self.lbuser3 = LBUSER3
c = self.time_coordinate_from_um_timeseries(axiscode,
'y')
else:
yc = self.xy_coordinate(axiscode, 'y')
#--- End: if
# ------------------------------------------------------------
# Create the 'X' dimension coordinate
# ------------------------------------------------------------
axiscode = ix
xc = None
if axiscode is not None:
if axiscode in (20, 23):
# X axis is time since reference date
if extra.get('x', None) is not None:
c = self.time_coordinate_from_extra_data(axiscode, 'x')
else:
LBUSER3 = int_hdr[lbuser3]
if LBUSER3 == LBNPT:
self.lbuser3 = LBUSER3
c = self.time_coordinate_from_um_timeseries(axiscode, 'x')
else:
xc = self.xy_coordinate(axiscode, 'x')
#--- End: if
# -10: rotated latitude (not an official axis code)
# -11: rotated longitude (not an official axis code)
if (iy, ix) == (-10, -11) or (iy, ix) == (-11, -10):
# ----------------------------------------------------
# Create a ROTATED_LATITUDE_LONGITUDE coordinate
# reference
# ----------------------------------------------------
transform = CoordinateReference(
name='rotated_latitude_longitude',
grid_north_pole_latitude=BPLAT,
grid_north_pole_longitude=BPLON,
coords=(_axis['y'], _axis['x']))
# --------------------------------------------------------
# Create UNROTATED, 2-D LATITUDE and LONGITUDE auxiliary
# coordinates
# --------------------------------------------------------
self.latitude_longitude_2d_aux_coordinates(yc, xc, transform)
# Insert the coordinate reference into the domain
self.domain.insert_ref(transform, copy=False)
#--- End: if
# ------------------------------------------------------------
# Create a RADIATION WAVELENGTH dimension coordinate
# ------------------------------------------------------------
try:
rwl, rwl_units = self.cf_info['below']
except (KeyError, TypeError):
pass
else:
c = self.radiation_wavelength_coordinate(rwl, rwl_units)
# Set LBUSER5 to zero so that it is not confused for a
# pseudolevel
LBUSER5 = 0
#--- End: try
# ------------------------------------------------------------
# Create a PSEUDOLEVEL dimension coordinate. This must be
# done *after* the possible creation of a radiation
# wavelength dimension coordinate.
# ------------------------------------------------------------
if LBUSER5 != 0:
self.pseudolevel_coordinate(LBUSER5)
attributes['int_hdr'] = int_hdr[:]
attributes['real_hdr'] = real_hdr[:]
attributes['file'] = filename
attributes['id'] = identity
cf_properties['Conventions'] = __Conventions__
cf_properties['runid'] = self.decode_lbexp()
cf_properties['lbproc'] = str(LBPROC)
cf_properties['lbtim'] = str(LBTIM)
cf_properties['stash_code'] = str(stash)
# ------------------------------------------------------------
# Create cell methods
# ------------------------------------------------------------
cell_methods = self.create_cell_methods()
if cell_methods is not None:
cf_properties['cell_methods'] = cell_methods
# ------------------------------------------------------------
# Set the data and extra data
# ------------------------------------------------------------
data = self.create_data()
cf_properties['_FillValue'] = data.fill_value
# ------------------------------------------------------------
# Create the field
# ------------------------------------------------------------
# Add kwargs to the CF properties
cf_properties.update(kwargs)
field = Field(domain=self.domain,
data=self.data,
axes=self.data_axes,
properties=cf_properties,
attributes=attributes,
copy=False)
# Check for decreasing axes that aren't decreasing
down_axes = self.down_axes
if down_axes:
field.flip(down_axes, i=True)
# Force cyclic X axis for paritcular values of LBHEM
if int_hdr[lbhem] in (0, 1, 2, 4):
field.cyclic('X', period=360)
self.fields.append(field)
#--- End: for
self._nonzero = True
#--- End: def
def __nonzero__(self):
'''
x.__nonzero__() <==> bool(x)
'''
return self._nonzero
#--- End: if
def __repr__(self):
'''
x.__repr__() <==> repr(x)
'''
return self.fdr()
#--- End: def
def __str__(self):
'''
x.__str__() <==> str(x)
'''
out = [self.fdr()]
attrs = ('endian',
'reftime', 'vtime', 'dtime',
'um_version', 'source',
'it', 'iz', 'ix', 'iy',
'site_time_cross_section', 'timeseries',
'file')
for attr in attrs:
out.append('%s=%s' % (attr, getattr(self, attr, None)))
out.append('')
return '\n'.join(out)
#--- End: def
def atmosphere_hybrid_height_coordinate(self, axiscode):
'''
**From appendix A of UMDP F3**
From UM Version 5.2, the method of defining the model levels in PP
headers was revised. At vn5.0 and 5.1, eta values were used in the PP
headers to specify the levels of model data, which was of limited use
when plotting data on model levels. From 5.2, the PP headers were
redefined to give information on the height of the level. Given a 2D
orography field, the height field for a given level can then be
derived. The height coordinates for PP-output are defined as:
Z(i,j,k)=Zsea(k)+C(k)*orography(i,j)
where Zsea(k) and C(k) are height based hybrid coefficients.
Zsea(k) = eta_value(k)*Height_at_top_of_model
C(k)=[1-eta_value(k)/eta_value(first_constant_rho_level)]**2 forlevels less than or equal to first_constant_rho_level
C(k)=0.0 for levels greater than first_constant_rho_level
where eta_value(k) is the eta_value for theta or rho level k. The
eta_value is a terrain-following height coordinate; full details are
given in UMDP15, Appendix B.
The PP headers store Zsea and C as follows :-
* 46 = bulev = brsvd1 = Zsea of upper layer boundary
* 52 = blev = Zsea of level
* 53 = brlev = Zsea of lower layer boundary
* 47 = bhulev = brsvd2 = C of upper layer boundary
* 54 = bhlev = C of level
* 55 = bhrlev = C of lower layer boundary
:Parameters:
axiscode : int
:Returns:
out : cf.DimensionCoordinate or None
'''
domain = self.domain
zdim = _axis['z']
# Insert new Z axis
domain.insert_axis(self.nz, key=zdim)
# "a" auxiliary coordinate
array = numpy_array([rec.real_hdr[blev] for rec in self.z_recs], # Zsea
dtype=float)
bounds0 = numpy_array([rec.real_hdr[brlev] for rec in self.z_recs], #Zsea lower
dtype=float)
bounds1 = numpy_array([rec.real_hdr[brsvd1] for rec in self.z_recs], #Zsea upper
dtype=float)
bounds = numpy_column_stack((bounds0, bounds1))
ac = AuxiliaryCoordinate()
ac = self.coord_data(ac, array, bounds, units=_Units['m'])
ac.id = 'UM_atmosphere_hybrid_height_coordinate_a'
ac.long_name = 'height based hybrid coeffient a'
key_a = domain.insert_aux(ac, axes=[zdim], copy=False)
# atmosphere_hybrid_height_coordinate dimension coordinate
TOA_height = bounds1.max()
if TOA_height <= 0:
TOA_height = self.height_at_top_of_model
if not TOA_height:
dc = None
else:
array = array / TOA_height
bounds = bounds / TOA_height
dc = DimensionCoordinate()
dc = self.coord_data(dc, array, bounds, units=_Units[''])
dc.standard_name = 'atmosphere_hybrid_height_coordinate'
dc = self.coord_axis(dc, axiscode)
dc = self.coord_positive(dc, axiscode, zdim)
domain.insert_dim(dc, key=zdim, copy=False)
#--- End: if
# "b" auxiliary coordinate
array = numpy_array([rec.real_hdr[bhlev] for rec in self.z_recs],
dtype=float)
bounds0 = numpy_array([rec.real_hdr[bhrlev] for rec in self.z_recs],
dtype=float)
bounds1 = numpy_array([rec.real_hdr[brsvd2] for rec in self.z_recs],
dtype=float)
bounds = numpy_column_stack((bounds0, bounds1))
ac = AuxiliaryCoordinate()
ac = self.coord_data(ac, array, bounds, units=_Units['1'])
ac.id = 'UM_atmosphere_hybrid_height_coordinate_b'
ac.long_name = 'height based hybrid coeffient b'
key_b = domain.insert_aux(ac, axes=[zdim], copy=False)
if bool(dc):
self.cell_method_axis_name['z'] = dc.identity()
# atmosphere_hybrid_height_coordinate coordinate reference
ref = CoordinateReference(
name='atmosphere_hybrid_height_coordinate',
a=key_a, b=key_b,
coords=(key_a, key_b), coord_terms=('a', 'b'))
self.domain.insert_ref(ref, copy=False)
#--- End: if
return dc
#--- End: def
def depth_coordinate(self, axiscode):
'''
:Parameters:
axiscode : int
:Returns:
out : cf.DimensionCoordinate or None
'''
dc = self.model_level_number_coordinate(aux=False)
domain = self.domain
zdim = _axis['z']
array = numpy_array([rec.real_hdr[blev] for rec in self.z_recs],
dtype=float)
bounds0 = numpy_array([rec.real_hdr[brlev] for rec in self.z_recs],
dtype=float)
bounds1 = numpy_array([rec.real_hdr[brsvd1] for rec in self.z_recs],
dtype=float)
bounds = numpy_column_stack((bounds0, bounds1))
ac = AuxiliaryCoordinate()
ac = self.coord_data(ac, array, bounds, units=_Units['m'])
ac.id = 'UM_atmosphere_hybrid_height_coordinate_ak'
ac.long_name = 'atmosphere_hybrid_height_coordinate_ak'
domain.insert_aux(ac, axes=[zdim], copy=False)
array = numpy_array([rec.real_hdr[bhlev] for rec in self.z_recs],
dtype=float)
bounds0 = numpy_array([rec.real_hdr[bhrlev] for rec in self.z_recs],
dtype=float)
bounds1 = numpy_array([rec.real_hdr[brsvd2] for rec in self.z_recs],
dtype=float)
bounds = numpy_column_stack((bounds0, bounds1))
ac = AuxiliaryCoordinate()
ac = self.coord_data(ac, array, bounds, units=_Units['1'])
ac.id = 'UM_atmosphere_hybrid_height_coordinate_bk'
ac.long_name = 'atmosphere_hybrid_height_coordinate_bk'
domain.insert_aux(ac, axes=[zdim], copy=False)
if dc:
self.cell_method_axis_name['z'] = dc.identity()
return dc
#--- End: def
def atmosphere_hybrid_sigma_pressure_coordinate(self, axiscode):
'''
atmosphere_hybrid_sigma_pressure_coordinate when not an array axis
:Parameters:
axiscode : int
:Returns:
out : cf.DimensionCoordinate
'''
# 46 BULEV Upper layer boundary or BRSVD(1)
#
# 47 BHULEV Upper layer boundary or BRSVD(2)
#
# For hybrid levels:
# - BULEV is B-value at half-level above.
# - BHULEV is A-value at half-level above.
#
# For hybrid height levels (vn5.2-, Smooth heights)
# - BULEV is Zsea of upper layer boundary
# * If rho level: Zsea for theta level above
# * If theta level: Zsea for rho level above
# - BHLEV is C of upper layer boundary
# * If rho level: C for theta level above
# * If theta level: C for rho level above
array = []
bounds = []
ak_array = []
ak_bounds = []
bk_array = []
bk_bounds = []
for rec in self.z_recs:
BLEV, BRLEV, BHLEV, BHRLEV, BULEV, BHULEV = self.header_bz(rec)
array.append(BLEV + BHLEV/_pstar)
bounds.append([BRLEV + BHRLEV/_pstar, BULEV + BHULEV/_pstar])
ak_array.append(BHLEV)
ak_bounds.append((BHRLEV, BHULEV))
bk_array.append(BLEV)
bk_bounds.append((BRLEV , BULEV))
#--- End: for
array = numpy_array(array , dtype=float)
bounds = numpy_array(bounds , dtype=float)
ak_array = numpy_array(ak_array , dtype=float)
ak_bounds = numpy_array(ak_bounds, dtype=float)
bk_array = numpy_array(bk_array , dtype=float)
bk_bounds = numpy_array(bk_bounds, dtype=float)
domain = self.domain
zdim = _axis['z']
dc = DimensionCoordinate()
dc = self.coord_data(
dc, array, bounds,
units=_axiscode_to_Units.setdefault(axiscode, None))
dc = self.coord_positive(dc, axiscode, zdim)
dc = self.coord_axis(dc, axiscode)
dc = self.coord_names(dc, axiscode)
domain.insert_dim(dc, key=zdim, copy=False)
ac = AuxiliaryCoordinate()
ac = self.coord_data(ac, ak_array, ak_bounds, units=_Units['Pa'])
ac.id = 'UM_atmosphere_hybrid_sigma_pressure_coordinate_ak'
ac.long_name = 'atmosphere_hybrid_sigma_pressure_coordinate_ak'
domain.insert_aux(ac, axes=[zdim], copy=False)
ac = AuxiliaryCoordinate()
ac = self.coord_data(ac, bk_array, bk_bounds, units=_Units['1'])
domain.insert_aux(ac, axes=[zdim], copy=False)
ac.id = 'UM_atmosphere_hybrid_sigma_pressure_coordinate_bk'
ac.long_name = 'atmosphere_hybrid_sigma_pressure_coordinate_bk'
self.cell_method_axis_name['z'] = dc.identity()
return dc
#--- End: def
def create_cell_methods(self):
'''Create the cell methods
'''
cell_methods = []
LBPROC = self.lbproc
LBTIM_IB = self.lbtim_ib
tmean_proc = 0
if LBTIM_IB in (2, 3) and LBPROC in (128, 192, 2176, 4224, 8320):
tmean_proc = 128
LBPROC -= 128
# ------------------------------------------------------------
# Area cell methods
# ------------------------------------------------------------
# -10: rotated latitude (not an official axis code)
# -11: rotated longitude (not an official axis code)
if self.ix in (10, 11, 12, -10, -11) and self.iy in (10, 11, 12, -10, -11):
cf_info = self.cf_info
if 'where' in cf_info:
cell_methods.append('area: mean')
cell_methods.append(cf_info['where'])
if 'over' in cf_info:
cell_methods.append(cf_info['over'])
#--- End: if
if LBPROC == 64:
cell_methods.append('x: mean')
# dch : do special zonal mean as as in pp_cfwrite
# ------------------------------------------------------------
# Vertical cell methods
# ------------------------------------------------------------
if LBPROC == 2048:
cell_methods.append('z: mean')
# ------------------------------------------------------------
# Time cell methods
# ------------------------------------------------------------
if LBTIM_IB == 0 or LBTIM_IB == 1:
cell_methods.append('t: point')
elif LBPROC == 4096:
cell_methods.append('t: minimum')
elif LBPROC == 8192:
cell_methods.append('t: maximum')
if tmean_proc == 128:
if LBTIM_IB == 2:
cell_methods.append('t: mean')
elif LBTIM_IB == 3:
cell_methods.append('t: mean within years')
cell_methods.append('t: mean over years')
#--- End: if
if not cell_methods:
return None
cell_methods = CellMethods(' '.join(cell_methods))
cell_method_axis_name = self.cell_method_axis_name
for c in cell_methods:
names0 = c.names[0]
c.axes = [_axis[name] for name in names0]
c.names = [cell_method_axis_name[name] for name in names0]
#--- End: for
return cell_methods
#--- End: def
def coord_axis(self, c, axiscode):
axis = _coord_axis.setdefault(axiscode, None)
if axis is not None:
c.axis = axis
return c
#--- End: def
def coord_data(self, c, array=None, bounds=None,
units=None, fill_value=None, climatology=False):
'''
Set the data array of a coordinate construct.
:Parameters:
c : cf.DimensionCoordinate or cf.AuxiliaryCoordinate
data : array-like, optional
The data array.
bounds : array-like, optional
The Cell bounds for the data array.
units : cf.Units, optional
The units of the data array.
fill_value : optional
climatology : bool, optional
Whether or not the coordinate construct is a time
climatology. By default it is not.
:Returns:
out : cf.Coordinate
'''
if array is not None:
array = Data(array, units=units, fill_value=fill_value)
if bounds is not None:
bounds = Data(bounds, units=units, fill_value=fill_value)
if climatology:
c.climatology = True
#--- End: if
c.insert_data(array, bounds=bounds, copy=False)
return c
#--- End: def
def coord_names(self, c, axiscode):
'''
'''
standard_name = _coord_standard_name.setdefault(axiscode, None)
if standard_name is not None:
c.setprop('standard_name', standard_name)
c.ncvar = standard_name
else:
long_name = _coord_long_name.setdefault(axiscode, None)
if long_name is not None:
c.long_name = long_name
return c
#--- End: def
def coord_positive(self, c, axiscode, dim):
positive = _coord_positive.setdefault(axiscode, None)
if positive is not None:
c.positive = positive
if positive == 'down' and axiscode != 4:
self.down_axes.add(dim)
#--- End: def
return c
#--- End: def
def ctime(self, rec):
'''
'''
reftime = self.refUnits
LBVTIME = tuple(self.header_vtime(rec))
LBDTIME = tuple(self.header_dtime(rec))
key = (LBVTIME, LBDTIME, self.refunits, self.calendar)
ctime = _cached_ctime.get(key, None)
if ctime is None:
# LTIME = list(LBDTIME)
# LTIME[0] = LBVTIME[0]
ctime = Datetime(*LBDTIME)
ctime.year = LBVTIME[0]
if ctime < Datetime(*LBVTIME):
ctime.year += 1
ctime = Data(ctime, reftime).array.item()
_cached_ctime[key] = ctime
#--- End: if
return ctime
#--- End: def
def header_vtime(self, rec):
'''
Return the list [LBYR, LBMON, LBDAT, LBHR, LBMIN] for the given
record.
:Parameters:
rec :
:Returns:
out : list
:Examples:
>>> u.header_vtime(rec)
[1991, 1, 1, 0, 0]
'''
return rec.int_hdr[lbyr:lbmin+1]
#--- End: def
def header_dtime(self, rec):
'''
Return the list [LBYRD, LBMOND, LBDATD, LBHRD, LBMIND] for the
given record.
:Parameters:
rec :
:Returns:
out : list
:Examples:
>>> u.header_dtime(rec)
[1991, 2, 1, 0, 0]
'''
return rec.int_hdr[lbyrd:lbmind+1]
#--- End: def
def header_bz(self, rec):
'''
Return the list [BLEV, BRLEV, BHLEV, BHRLEV, BULEV, BHULEV] for the
given record.
:Parameters:
rec :
:Returns:
out : list
:Examples:
>>> u.header_bz(rec)
'''
real_hdr = rec.real_hdr
return (real_hdr[blev:bhrlev+1].tolist() + # BLEV, BRLEV, BHLEV, BHRLEV
real_hdr[brsvd1:brsvd2+1].tolist()) # BULEV, BHULEV
#--- End: def
def header_lz(self, rec):
'''
Return the list [LBLEV, LBUSER5] for the given record.
:Parameters:
rec :
:Returns:
out : list
:Examples:
>>> u.header_lz(rec)
'''
int_hdr = rec.int_hdr
return [int_hdr.item(lblev,), int_hdr.item(lbuser5,)]
#--- End: def
def header_z(self, rec):
'''
Return the list [LBLEV, LBUSER5, BLEV, BRLEV, BHLEV, BHRLEV, BULEV,
BHULEV] for the given record.
:Parameters:
rec :
:Returns:
out : list
:Examples:
>>> u.header_z(rec)
'''
# ------------------------------------------------------------
# These header items are used by the compare_levels function
# in compare.c
# ------------------------------------------------------------
return self.header_lz + self.header_bz
#--- End: def
def create_data(self):
'''
Sets the `!data` and `!data_axes` attributes.
:Returns:
None
'''
LBROW = self.lbrow
LBNPT = self.lbnpt
yx_shape = (LBROW, LBNPT)
yx_size = LBROW * LBNPT
nz = self.nz
nt = self.nt
recs = self.recs
units = self.um_Units
data_type_in_file = self.data_type_in_file
filename = self.filename
data_axes = [_axis['y'], _axis['x']]
if len(recs) == 1:
# --------------------------------------------------------
# 0-d partition matrix
# --------------------------------------------------------
rec = recs[0]
data = Data(UMFileArray(file=filename,
ndim=2,
shape=yx_shape,
size=yx_size,
dtype=data_type_in_file(rec),
header_offset=rec.hdr_offset,
data_offset=rec.data_offset,
disk_length=rec.disk_length),
units=units,
fill_value=rec.real_hdr.item(bmdi,))
else:
# --------------------------------------------------------
# 1-d or 2-d partition matrix
# --------------------------------------------------------
file_data_types = set()
word_sizes = set()
# Find the partition matrix shape
pmshape = [n for n in (nt, nz) if n > 1]
pmndim = len(pmshape)
partitions = []
empty_list = []
partitions_append = partitions.append
zero_to_LBROW = (0, LBROW)
zero_to_LBNPT = (0, LBNPT)
if pmndim == 1:
# ----------------------------------------------------
# 1-d partition matrix
# ----------------------------------------------------
data_ndim = 3
if nz > 1:
pmaxes = [_axis[self.z_axis]]
data_shape = (nz, LBROW, LBNPT)
data_size = nz * yx_size
else:
pmaxes = [_axis['t']]
data_shape = (nt, LBROW, LBNPT)
data_size = nt * yx_size
partition_shape = [1, LBROW, LBNPT]
for i, rec in enumerate(recs):
# Find the data type of the array in the file
file_data_type = data_type_in_file(rec)
file_data_types.add(file_data_type)
subarray = UMFileArray(file=filename,
ndim=2,
shape=yx_shape,
size=yx_size,
dtype=file_data_type,
header_offset=rec.hdr_offset,
data_offset=rec.data_offset,
disk_length=rec.disk_length)
partitions_append(Partition(
subarray = subarray,
location = [(i, i+1), zero_to_LBROW, zero_to_LBNPT],
shape = partition_shape,
axes = data_axes,
flip = empty_list,
part = empty_list,
Units = units))
#--- End: for
# Populate the 1-d partition matrix
matrix = numpy_array(partitions, dtype=object)
else:
# ----------------------------------------------------
# 2-d partition matrix
# ----------------------------------------------------
pmaxes = [_axis['t'], _axis[self.z_axis]]
data_shape = (nt, nz, LBROW, LBNPT)
data_size = nt * nz * yx_size
data_ndim = 4
partition_shape = [1, 1, LBROW, LBNPT]
for i, rec in enumerate(recs):
# Find T and Z axis indices
t, z = divmod(i, nz)
# Find the data type of the array in the file
file_data_type = data_type_in_file(rec)
file_data_types.add(file_data_type)
subarray = UMFileArray(file=filename,
ndim=2,
shape=yx_shape,
size=yx_size,
dtype=file_data_type,
header_offset=rec.hdr_offset,
data_offset=rec.data_offset,
disk_length=rec.disk_length)
partitions_append(Partition(
subarray=subarray,
location=[(t, t+1), (z, z+1), zero_to_LBROW, zero_to_LBNPT],
shape=partition_shape,
axes=data_axes,
flip=empty_list,
part=empty_list,
Units=units))
#--- End: for
# Populate the 2-d partition matrix
matrix = numpy_array(partitions, dtype=object)
matrix.resize(pmshape)
#--- End: if
data_axes = pmaxes + data_axes
# Set the data array
data = Data(units=units, fill_value=recs[0].real_hdr.item(bmdi,))
data._axes = data_axes
data._shape = data_shape
data._ndim = data_ndim
data._size = data_size
data.partitions = PartitionMatrix(matrix, pmaxes)
data.dtype = numpy_result_type(*file_data_types)
#--- End: if
self.data = data
self.data_axes = data_axes
return data
#---End: def
def decode_lbexp(self):
'''Decode the integer value of LBEXP in the PP header into a runid.
If this value has already been decoded, then it will be returned from
the cache, otherwise the value will be decoded and then added to the
cache.
:Returns:
out : str
A string derived from LBEXP. If LBEXP is a negative integer
then that number is returned as a string.
:Examples:
>>> self.decode_lbexp()
'aaa5u'
>>> self.decode_lbexp()
'-34'
'''
LBEXP = self.int_hdr[lbexp]
runid = _cached_runid.get(LBEXP, None)
if runid is not None:
# Return a cached decoding of this LBEXP
return runid
if LBEXP < 0:
runid = str(LBEXP)
else:
# Convert LBEXP to a binary string, filled out to 30 bits with
# zeros
bits = bin(LBEXP)
bits = bits.lstrip('0b').zfill(30)
# Step through 6 bits at a time, converting each 6 bit chunk into
# a decimal integer, which is used as an index to the characters
# lookup list.
runid = []
for i in xrange(0,30,6):
index = int(bits[i:i+6], 2)
if index < _n_characters:
runid.append(_characters[index])
#--- End: for
runid = ''.join(runid)
#--- End: def
# Enter this runid into the cache
_cached_runid[LBEXP] = runid
# Return the runid
return runid
#--- End: def
def dtime(self, rec):
'''
'''
reftime = self.refUnits
units = self.refunits
calendar = self.calendar
LBDTIME = tuple(self.header_dtime(rec))
key = (LBDTIME, units, calendar)
time = _cached_date2num.get(key, None)
if time is None:
# It is important to use the same time_units as vtime
if self.calendar == 'gregorian':
time = netCDF4_date2num(
datetime(*LBDTIME), units, calendar)
else:
time = netCDF4_date2num(
netCDF4_netcdftime_datetime(*LBDTIME), units, calendar)
_cached_date2num[key] = time
#--- End: if
return time
#--- End: def
def fdr(self):
'''Return a the contents of PP field headers as strings.
This is a bit like printfdr in the UKMO IDL PP library.
:Returns:
out : list
'''
out2 = []
for i, rec in enumerate(self.recs):
out = ['Field %d:' % i]
x = ['%s::%s' % (name, value)
for name, value in zip(_header_names,
self.int_hdr + self.real_hdr)]
x = textwrap.fill(' '.join(x), width=79)
out.append(x.replace('::', ': '))
if self.extra:
out.append('EXTRA DATA:')
for key in sorted(self.extra):
out.append('%s: %s' % (key, str(self.extra[key])))
#--- End: if
out.append('file: '+self.filename)
out.append('format, byte order, word size: %s, %s, %d' %
(self.fmt, self.byte_ordering, self.word_size))
out.append('')
out2.append('\n'.join(out))
#--- End: for
return out2
#--- End: def
def latitude_longitude_2d_aux_coordinates(self, yc, xc, transform):
'''
'''
BDX = self.bdx
BDY = self.bdy
LBNPT = self.lbnpt
LBROW = self.lbrow
BPLAT = self.bplat
BPLON = self.bplon
# Create the unrotated latitude and longitude arrays if we
# couldn't find them in the cache
cache_key = (LBNPT, LBROW, BDX, BDY, BPLAT, BPLON)
lat, lon = _cache_latlon.get(cache_key, (None, None))
if lat is None:
lat, lon = self.unrotated_latlon(yc.varray, xc.varray,
BPLAT, BPLON)
atol = self.atol
if abs(BDX) >= atol and abs(BDY) >= atol:
_cache_latlon[cache_key] = (lat, lon)
#--- End: if
# if xc.hasbounds and yc.hasbounds:
# cache_key = ('bounds',) + cache_key
# lat_bounds, lon_bounds = _cache_latlon.get(cache_key, (None, None))
# print lat_bounds
# if lat_bounds is None:
# print 'CALC BOUNDS'
# xb = numpy_empty(xc.size+1)
# yb = numpy_empty(yc.size+1)
# xb[:-1] = xc.bounds.subspace[ :, 0].squeeze(1, i=True).array
# xb[-1 ] = xc.bounds.subspace[-1, 1].squeeze(1, i=True).array
# yb[:-1] = yc.bounds.subspace[ :, 0].squeeze(1, i=True).array
# yb[-1 ] = yc.bounds.subspace[-1, 1].squeeze(1, i=True).array
#
# lat_bounds, lon_bounds = self.unrotated_latlon(yb, xb, BPLAT, BPLON)
#
# print lat_bounds
# print lat_bounds.shape
# yyy = numpy_empty(lat.shape + (4,))
#
#
#
# print lat.shape, yyy.shape
#
# atol = self.atol
# if abs(BDX) >= atol and abs(BDY) >= atol:
# _cache_latlon[cache_key] = (lat, lon)
#--- End: if
axes = [_axis['y'], _axis['x']]
for axiscode, array in zip((10, 11),
(lat, lon)):
ac = AuxiliaryCoordinate()
ac = self.coord_data(ac, array,
units=_axiscode_to_Units.setdefault(axiscode, None))
ac = self.coord_names(ac, axiscode)
key = self.domain.insert_aux(ac, axes=axes, copy=False)
transform.coords.add(key)
#--- End: for
#--- End: def
def model_level_number_coordinate(self, aux=False):
'''model_level_number dimension or auxiliary coordinate
:Parameters:
aux : bool
:Returns:
out : cf.AuxiliaryCoordinate or cf.DimensionCoordinate or None
'''
array = tuple([rec.int_hdr.item(lblev,) for rec in self.z_recs])
key = array
c = _cached_model_level_number_coordinate.get(key, None)
if c is not None:
if aux:
self.domain.insert_aux(c, axes=[_axis['z']], copy=True)
else:
self.domain.insert_dim(c, key=_axis['z'], copy=True)
self.cell_method_axis_name['z'] = c.identity()
else:
array = numpy_array(array, dtype=self.int_hdr_dtype)
if array.min() < 0:
return
array = numpy_where(array==9999, 0, array)
axiscode = 5
if aux:
c = AuxiliaryCoordinate()
c = self.coord_data(c, array, units=Units('1'))
c = self.coord_names(c, axiscode)
self.domain.insert_aux(c, axes=[_axis['z']], copy=False)
else:
c = DimensionCoordinate()
c = self.coord_data(c, array, units=Units('1'))
c = self.coord_names(c, axiscode)
c = self.coord_axis(c, axiscode)
self.domain.insert_dim(c, key=_axis['z'], copy=False)
self.cell_method_axis_name['z'] = c.identity()
#--- End: if
_cached_model_level_number_coordinate[key] = c
#--- End: if
return c
#--- End: def
def data_type_in_file(self, rec):
'''Return the data type of the data array.
:Parameters:
rec : umfile.Rec
:Returns:
out : numpy.dtype
:Examples:
'''
# Find the data type
if rec.int_hdr.item(lbuser2,) == 3:
# Boolean
return numpy_dtype(bool)
else:
# Int or float
return rec.get_type_and_num_words()[0]
# rec_file = rec.file
## data_type = rec_file.c_interface.get_type_and_length(
# data_type = rec_file.c_interface.get_type_and_num_words(rec.int_hdr)[0]
# if data_type == 'int':
# # Integer
# data_type = 'int%d' % (rec_file.word_size * 8)
# else:
# # Float
# data_type = 'float%d' % (rec_file.word_size * 8)
# #--- End: if
#
# return numpy_dtype(data_type)
#--- End: def
def printfdr(self):
'''Print out the contents of PP field headers.
This is a bit like printfdr in the UKMO IDL PP library.
:Examples:
>>> u.printfdr()
'''
for header in self.fdr():
print header
#--- End: def
def pseudolevel_coordinate(self, LBUSER5):
'''
'''
if self.nz == 1:
array = numpy_array((LBUSER5,), dtype=self.int_hdr_dtype)
else:
# 'Z' aggregation has been done along the pseudolevel axis
array = numpy_array([rec.int_hdr.item(lbuser5,)
for rec in self.z_recs],
dtype=self.int_hdr_dtype)
self.z_axis = 'p'
#--- End: if
axiscode = 40
dc = DimensionCoordinate()
dc = self.coord_data(
dc, array,
units=_axiscode_to_Units.setdefault(axiscode, None))
dc.long_name = 'pseudolevel' # for PP stash_code %d' % self.stash
dc.id = 'UM_pseudolevel'
self.domain.insert_dim(dc, key=_axis['p'], copy=False)
self.cell_method_axis_name['p'] = dc.identity()
return dc
#--- End: def
def radiation_wavelength_coordinate(self, rwl, rwl_units):
'''
'''
array = numpy_array((rwl,), dtype=float)
bounds = numpy_array(((0.0, rwl)), dtype=float)
units = _Units.get(rwl_units, None)
if units is None:
units = Units(rwl_units)
_Units[rwl_units] = units
axiscode = -20
dc = DimensionCoordinate()
dc = self.coord_data(dc, array, bounds, units=units)
dc = self.coords_names(dc, axiscode)
self.domain.insert_dim(dc, key=_axis['r'], copy=False)
self.cell_method_axis_name['r'] = dc.identity()
return dc
#--- End: def
def reference_time_Units(self):
'''
'''
time_units = 'days since %d-1-1' % self.int_hdr[lbyr]
calendar = self.calendar
key = time_units+' calendar='+calendar
units = _Units.get(key, None)
if units is None:
units = Units(time_units, calendar)
_Units[key] = units
#--- End: if
self.refUnits = units
self.refunits = time_units
return units
#--- End: def
def size_1_height_coordinate(self, axiscode, height, units):
# Create the height coordinate from the information given in the
# STASH to standard_name conversion table
key = (axiscode, height, units)
dc = _cached_size_1_height_coordinate.get(key, None)
zdim = _axis['z']
if dc is not None:
copy = True
else:
height_units = _Units.get(units, None)
if height_units is None:
height_units = Units(units)
_Units[units] = height_units
array = numpy_array((height,), dtype=float)
dc = DimensionCoordinate()
dc = self.coord_data(dc, array, units=height_units)
dc = self.coord_positive(dc, axiscode, zdim)
dc = self.coord_axis(dc, axiscode)
dc = self.coord_names(dc, axiscode)
_cached_size_1_height_coordinate[key] = dc
copy = False
#--- End: def
self.domain.insert_dim(dc, key=zdim, copy=copy)
self.cell_method_axis_name['z'] = dc.identity()
return dc
#--- End: def
def test_um_condition(self, um_condition, LBCODE, BPLAT, BPLON):
'''Return True if a field satisfies the condition specified for a
STASH code to standard name conversion.
:Parameters:
um_condition : str
LBCODE : int
BPLAT : float
BPLON : float
:Returns:
out : bool
True if a field satisfies the condition specified, False
otherwise.
:Examples:
>>> ok = u.test_um_condition('true_latitude_longitude', ...)
'''
if um_condition == 'true_latitude_longitude':
if LBCODE in _true_latitude_longitude_lbcodes:
return True
# Check pole location in case of incorrect LBCODE
atol = self.atol
if (abs(BPLAT-90.0) <= atol + RTOL()*90.0 and
abs(BPLON) <= atol):
return True
elif um_condition == 'rotated_latitude_longitude':
if LBCODE in _rotated_latitude_longitude_lbcodes:
return True
# Check pole location in case of incorrect LBCODE
atol = self.atol
if not (abs(BPLAT-90.0) <= atol + RTOL()*90.0 and
abs(BPLON) <= atol):
return True
else:
raise ValueError(
"Unknown UM condition in STASH code conversion table: '%s'" %
um_condition)
# Still here? Then the condition has not been satisfied.
return
#--- End: def
def test_um_version(self, valid_from, valid_to, um_version):
'''Return True if the UM version applicable to tghis field is
within the given range.
If possible, the UM version is derived from the PP header and stored
in the metadata object. Otherwise it is taken from the *um_version*
parameter.
:Parameters:
valid_from : int, float or None
valid_to : int, float or None
um_version : int or float
:Returns:
out : bool
True if the UM version applicable to this field is within the
range, False otherwise.
:Examples:
>>> ok = u.test_um_version(401, 505, 1001)
>>> ok = u.test_um_version(401, None, 606.3)
>>> ok = u.test_um_version(None, 405, 401)
'''
if valid_to is None:
if valid_from <= um_version:
return True
elif valid_from is None:
if um_version <= valid_to:
return True
elif valid_from <= um_version <= valid_to:
return True
return False
# if valid_from is '':
# valid_from = None
#
# if valid_to is '':
# if valid_from <= um_version:
# return True
# elif valid_from <= um_version <= valid_to:
# return True
#
# return False
#--- End: def
def time_coordinate(self, axiscode):
'''
Return the T dimension coordinate
'''
recs = self.t_recs
vtimes = numpy_array([self.vtime(rec) for rec in recs], dtype=float)
dtimes = numpy_array([self.dtime(rec) for rec in recs], dtype=float)
IB = self.lbtim_ib
if IB <= 1 or vtimes.item(0,) >= dtimes.item(0,):
array = vtimes
bounds = None
climatology = False
elif IB == 3:
# The field is a time mean from T1 to T2 for each year
# from LBYR to LBYRD
ctimes = numpy_array([self.ctime(rec) for rec in recs])
array = 0.5*(vtimes + ctimes)
bounds = numpy_column_stack((vtimes, dtimes))
climatology = True
else:
array = 0.5*(vtimes + dtimes)
bounds = numpy_column_stack((vtimes, dtimes))
climatology = False
#--- End: if
dc = DimensionCoordinate()
dc = self.coord_data(dc, array, bounds,
units=self.refUnits,
climatology=climatology)
dc = self.coord_axis(dc, axiscode)
dc = self.coord_names(dc, axiscode)
self.domain.insert_dim(dc, key=_axis['t'], copy=False)
self.cell_method_axis_name['t'] = dc.identity()
return dc
#--- End: def
def time_coordinate_from_extra_data(self, axiscode, axis):
'''
'''
extra = self.extra
array = extra[axis]
bounds = extra.get(axis+'_bounds', None)
calendar = self.calendar
if calendar == '360_day':
units = _Units['360_day 0-1-1']
elif calendar == 'gregorian':
units = _Units['gregorian 1752-9-13']
elif calendar == '365_day':
units = _Units['365_day 1752-9-13']
else:
units = None
dc = DimensionCoordinate()
dc = self.coord_data(dc, array, bounds, units=units)
dc = self.coord_axis(dc, axiscode)
dc = self.coord_names(dc, axiscode)
self.domain.insert_dim(dc, key=_axis[axis], copy=False)
self.cell_method_axis_name[axis] = dc.identity()
self.cell_method_axis_name['t'] = self.cell_method_axis_name[axis]
return dc
#--- End: def
def time_coordinate_from_um_timeseries(self, axiscode, axis):
# This PP/FF field is a timeseries. The validity time is
# taken to be the time for the first sample, the data time
# for the last sample, with the others evenly between.
rec = self.recs[0]
vtime = self.vtime(rec)
dtime = self.dtime(rec)
size = self.lbuser3 - 1.0
delta = (dtime - vtime)/size
array = numpy_arange(vtime, vtime+delta*size, size, dtype=float)
dc = DimensionCoordinate()
dc = self.coord_data(dc, array, units=units)
dc = self.coord_axis(dc, axiscode)
dc = self.coord_names(dc, axiscode)
self.domain.insert_dim(dc, key=_axis[axis], copy=False)
self.cell_method_axis_name['t'] = dc.identity()
return dc
#--- End: def
def vtime(self, rec):
'''
'''
reftime = self.refUnits
units = self.refunits
calendar = self.calendar
# LBVTIME = tuple(rec.int_hdr[lbyr: lbmin+1])
LBVTIME = tuple(self.header_vtime(rec))
key = (LBVTIME, units, calendar)
time = _cached_date2num.get(key, None)
if time is None:
# It is important to use the same time_units as dtime
if self.calendar == 'gregorian':
time = netCDF4_date2num(
datetime(*LBVTIME), units, calendar)
else:
time = netCDF4_date2num(
netCDF4_netcdftime_datetime(*LBVTIME), units, calendar)
_cached_date2num[key] = time
#--- End: if
return time
#--- End: def
def dddd(self):
for axis_code, extra_type in zip((11 , 10 ),
('x', 'y')):
coord_type = extra_type + '_domain_bounds'
if coord_type in p.extra:
p.extra[coord_type]
# Create, from extra data, an auxiliary coordinate should
# with 1) data and bounds, if the upper and lower be
# bounds have no missing values; or 2) data but no the
# bounds, if the upper bound has missing values axis
# but the lower bound does not. # which
file_position = ppfile.tell() # has
bounds = p.extra[coord_type][...] # axis_code
# Reset the file pointer after reading the extra # 13
# data into a numpy array
ppfile.seek(file_position, os.SEEK_SET)
data = None
if numpy_any(bounds[..., 1] == _pp_rmdi): # dch also test in bmdi?
if not numpy_any(bounds[...,0] == _pp_rmdi): # dch also test in bmdi?
data = bounds[...,0]
bounds = None
else:
data = numpy_mean(bounds, axis=1)
if (data, bounds) != (None, None):
aux = 'aux%(auxN)d' % locals()
auxN += 1 # Increment auxiliary number
coord = _create_Coordinate(domain, aux, axis_code, p=p,
array = data,
aux=True,
bounds_array = bounds,
pubattr = {'axis': None},
dimensions = [xdim]) # DCH
# xdim?
# should
# be
# the
# axis
# which
# has
# axis_code
# 13
#--- End: if
else:
coord_type = '%s_domain_lower_bound' % extra_type
if coord_type in p.extra:
# Create, from extra data, an auxiliary
# coordinate with data but no bounds, if the
# data noes not contain any missing values
file_position = ppfile.tell()
data = p.extra[coord_type][...]
# Reset the file pointer after reading the
# extra data into a numpy array
ppfile.seek(file_position, os.SEEK_SET)
if not numpy_any(data == _pp_rmdi): # dch also test in bmdi?
aux = 'aux%(auxN)d' % locals()
auxN += 1 # Increment auxiliary number
coord = _create_Coordinate(domain, aux, axis_code, p=p,
aux=True,
array=numpy_array(data),
pubattr={'axis': None},
dimensions=[xdim])# DCH xdim?
#--- End: if
#--- End: for
#--- End: if
# --------------------
def unrotated_latlon(self, rotated_lat, rotated_lon, pole_lat, pole_lon):
'''
Create 2-d arrays of unrotated latitudes and longitudes.
:Parameters:
rotated_lat, rotated_lon, pole_lat, pole_lon
'''
# Make sure rotated_lon and pole_lon is in [0, 360)
pole_lon = pole_lon % 360.0
# Convert everything to radians
pole_lon *= _pi_over_180
pole_lat *= _pi_over_180
cos_pole_lat = numpy_cos(pole_lat)
sin_pole_lat = numpy_sin(pole_lat)
# Create appropriate copies of the input rotated arrays
rot_lon = rotated_lon.copy()
rot_lat = rotated_lat.view()
# Make sure rotated longitudes are between -180 and 180
rot_lon %= 360.0
rot_lon = numpy_where(rot_lon < 180.0, rot_lon, rot_lon-360)
# Create 2-d arrays of rotated latitudes and longitudes in radians
nlat = rot_lat.size
nlon = rot_lon.size
rot_lon = numpy_resize(numpy_deg2rad(rot_lon), (nlat, nlon))
rot_lat = numpy_resize(numpy_deg2rad(rot_lat), (nlon, nlat))
rot_lat = numpy_transpose(rot_lat, axes=(1,0))
# Find unrotated latitudes
CPART = numpy_cos(rot_lon) * numpy_cos(rot_lat)
sin_rot_lat = numpy_sin(rot_lat)
x = cos_pole_lat * CPART + sin_pole_lat * sin_rot_lat
x = numpy_clip(x, -1.0, 1.0)
unrotated_lat = numpy_arcsin(x)
# Find unrotated longitudes
x = -cos_pole_lat*sin_rot_lat + sin_pole_lat*CPART
x /= numpy_cos(unrotated_lat) # dch /0 or overflow here? surely
# lat could be ~+-pi/2? if so,
# does x ~ cos(lat)?
x = numpy_clip(x, -1.0, 1.0)
unrotated_lon = -numpy_arccos(x)
unrotated_lon = numpy_where(rot_lon > 0.0,
-unrotated_lon, unrotated_lon)
if pole_lon >= self.atol:
SOCK = pole_lon - numpy_pi
else:
SOCK = 0
unrotated_lon += SOCK
# Convert unrotated latitudes and longitudes to degrees
unrotated_lat = numpy_rad2deg(unrotated_lat)
unrotated_lon = numpy_rad2deg(unrotated_lon)
# Return unrotated latitudes and longitudes
return unrotated_lat, unrotated_lon
#--- End: def
def xy_coordinate(self, axiscode, axis):
'''
Create an X or Y dimension coordinate from header entries or extra
data.
:Parameters:
axiscode : int
axis : str
'x' or 'y'
:Returns:
out : cf.DimensionCoordinate
'''
if axis == 'y':
delta = self.bdy
origin = self.real_hdr[bzy]
size = self.lbrow
else:
delta = self.bdx
origin = self.real_hdr[bzx]
size = self.lbnpt
if abs(delta) > self.atol:
# Create regular coordinates from header items
if axiscode == 11 or axiscode == -11:
origin -= divmod(origin + delta*size, 360.0)[0] * 360
while origin + delta*size > 360.0:
origin -= 360.0
while origin + delta*size < -360.0:
origin += 360.0
#--- End: if
array = numpy_arange(origin+delta, origin+delta*(size+0.5), delta,
dtype=float)
# Create the coordinate bounds
if axiscode in (13, 31, 40, 99):
# The following axiscodes do not have bounds:
# 13 = Site number (set of parallel rows or columns
# e.g.Time series)
# 31 = Logarithm to base 10 of pressure in mb
# 40 = Pseudolevel
# 99 = Other
bounds = None
else:
delta_by_2 = 0.5 * delta
bounds = numpy_empty((size, 2), dtype=float)
bounds[:, 0] = array - delta_by_2
bounds[:, 1] = array + delta_by_2
else:
# Create coordinate from extra data
array = self.extra.get(axis, None)
bounds = self.extra.get(axis+'_bounds', None)
#--- End: if
dc = DimensionCoordinate()
dc = self.coord_data(
dc, array, bounds,
units=_axiscode_to_Units.setdefault(axiscode, None))
dc = self.coord_positive(dc, axiscode, _axis[axis])
dc = self.coord_axis(dc, axiscode)
dc = self.coord_names(dc, axiscode)
self.domain.insert_dim(dc, key=_axis[axis], copy=False)
self.cell_method_axis_name[axis] = dc.identity()
return dc
#--- End: def
def z_coordinate(self, axiscode):
'''Create a Z dimension coordinate from BLEV
:Parameters:
axiscode : int
:Returns:
out : cf.DimensionCoordinate
'''
z_recs = self.z_recs
array = tuple([rec.real_hdr.item(blev,) for rec in z_recs])
bounds0 = tuple([rec.real_hdr[brlev] for rec in z_recs]) # lower level boundary
bounds1 = tuple([rec.real_hdr[brsvd1] for rec in z_recs]) # bulev
if _coord_positive.get(axiscode, None) == 'down':
bounds0, bounds1 = bounds1, bounds0
# key = (axiscode, array, bounds0, bounds1)
# dc = _cached_z_coordinate.get(key, None)
# if dc is not None:
# copy = True
# else:
copy = False
array = numpy_array(array, dtype=float)
bounds0 = numpy_array(bounds0, dtype=float)
bounds1 = numpy_array(bounds1, dtype=float)
bounds = numpy_column_stack((bounds0, bounds1))
if (bounds0 == bounds1).all():
bounds = None
else:
bounds = numpy_column_stack((bounds0, bounds1))
dc = DimensionCoordinate()
dc = self.coord_data(
dc, array,
bounds=bounds,
units=_axiscode_to_Units.setdefault(axiscode, None))
dc = self.coord_positive(dc, axiscode, _axis['z'])
dc = self.coord_axis(dc, axiscode)
dc = self.coord_names(dc, axiscode)
# _cached_z_coordinate[key] = dc
# #--- End: if
self.domain.insert_dim(dc, key=_axis['z'], copy=copy)
self.cell_method_axis_name['z'] = dc.identity()
return dc
#--- End: def
def z_reference_coordinate(self, axiscode):
'''
'''
array = numpy_array([rec.real_hdr.item(brlev,) for rec in self.z_recs],
dtype=float)
LBVC = self.lbvc
key = (axiscode, LBVC, array)
dc = _cached_z_reference_coordinate.get(key, None)
if dc is not None:
copy = True
else:
if not 128 <= LBVC <= 139:
bounds = []
for rec in self.z_recs:
BRLEV = rec.real_hdr.item(brlev,)
BRSVD1 = rec.real_hdr.item(brsvd1,)
if abs(BRSVD1-BRLEV) >= ATOL:
bounds = None
break
bounds.append((BRLEV, BRSVD1))
#--- End: for
else:
bounds = None
if bounds:
bounds = numpy_array((bounds,), dtype=float)
dc = DimensionCoordinate()
dc = self.coord_data(
dc, array, bounds,
units=_axiscode_to_Units.setdefault(axiscode, None))
dc = self.coord_axis(dc, axiscode)
dc = self.coord_names(dc, axiscode)
if not dc.get('positive', True): # ppp
dc.flip(i=True)
_cached_z_reference_coordinate[key] = dc
copy = False
#--- End: def
self.domain.insert_dim(dc, key=_axis['z'], copy=copy)
return dc
#--- End: def
#--- End: class
_stash2standard_name = {}
def load_stash2standard_name(table=None, delimiter='!'):
'''Load a STASH to standard name conversion table.
:Parameters:
table : str, optional
Use the conversion table at this file location. By default the
table will be looked for at
``os.path.join(os.path.dirname(cf.__file__),'etc/STASH_to_CF.txt')``
delimiter : str, optional
The delimiter of the table columns. By default, ``!`` is taken
as the delimiter.
:Returns:
None
*Examples:*
>>> load_stash2standard_name()
>>> load_stash2standard_name('my_table.txt')
>>> load_stash2standard_name('my_table2.txt', ',')
'''
# 0 Model
# 1 STASH code
# 2 STASH name
# 3 units
# 4 valid from UM vn
# 5 valid to UM vn
# 6 standard_name
# 7 CF extra info
# 8 PP extra info
if table is None:
# Use default conversion table
package_path = os.path.dirname(__file__)
table = os.path.join(package_path, 'etc/STASH_to_CF.txt')
#--- End: if
lines = csv.reader(open(table, 'r'),
delimiter=delimiter, skipinitialspace=True)
raw_list = []
[raw_list.append(line) for line in lines]
# Get rid of comments
for line in raw_list[:]:
if line[0].startswith('#'):
raw_list.pop(0)
continue
break
#--- End: for
# Convert to a dictionary which is keyed by (submodel, STASHcode)
# tuples
(model, stash, name,
units,
valid_from, valid_to,
standard_name, cf, pp) = range(9)
stash2sn = {}
for x in raw_list:
key = (int(x[model]), int(x[stash]))
if not x[units]:
x[units] = None
try:
cf_info = {}
if x[cf]:
for d in x[7].split():
if d.startswith('height='):
cf_info['height'] = re.split(_number_regex, d,
re.IGNORECASE)[1:4:2]
if cf_info['height'] == '':
cf_info['height'][1] = '1'
if d.startswith('below_'):
cf_info['below'] = re.split(_number_regex, d,
re.IGNORECASE)[1:4:2]
if cf_info['below'] == '':
cf_info['below'][1] = '1'
if d.startswith('where_'):
cf_info['where'] = d.replace('where_', 'where ', 1)
if d.startswith('over_'):
cf_info['over'] = d.replace('over_', 'over ', 1)
x[cf] = cf_info
except IndexError:
pass
try:
x[valid_from] = float(x[valid_from])
except ValueError:
x[valid_from] = None
try:
x[valid_to] = float(x[valid_to])
except ValueError:
x[valid_to] = None
x[pp] = x[pp].rstrip()
line = (x[name:],)
if key in stash2sn:
stash2sn[key] += line
else:
stash2sn[key] = line
#--- End: for
_stash2standard_name.clear()
_stash2standard_name.update(stash2sn)
# return stash2sn
#--- End: def
# ---------------------------------------------------------------------
# Create the STASH code to standard_name conversion dictionary
# ---------------------------------------------------------------------
#_stash2standard_name = load_stash2standard_name()
load_stash2standard_name()
def read(filename, um_version=405, verbose=False, aggregate=True,
byte_ordering=None, word_size=None, set_standard_name=True,
height_at_top_of_model=None):
'''Read fields from a PP file or UM fields file.
The file may be big or little endian, 32 or 64 bit
:Parameters:
filename : file or str
A string giving the file name, or an open file object, from
which to read fields.
um_version : number, optional
The Unified Model (UM) version to be used when decoding the PP
header. Valid versions are, for example, ``402`` (v4.2),
``606.3`` (v6.6.3) and ``1001`` (v10.1). The default version
is ``405`` (v4.5). The version is ignored if it can be
inferred from the PP headers, which will generally be the case
for files created at versions 5.3 and later. Note that the PP
header can not encode tertiary version elements (such as the
``3`` in ``606.3``), so it may be necessary to provide a UM
version in such cases.
verbose : bool, optional
set_standard_name : bool, optional
:Returns:
out : FieldList
The fields in the file.
:Examples:
>>> f = read('file.pp')
>>> f = read('*/file[0-9].pp', um_version=708)
'''
history = 'Converted from UM by cf-python v%s' % __version__
f = _open_um_file(filename)
# print 'um.read.read.py um_version=', repr(um_version)
um = [UMField(var, f.format, f.byte_ordering, f.word_size,
um_version, set_standard_name, history=history,
height_at_top_of_model=height_at_top_of_model)
for var in f.vars]
# # Clear the cache of unrotated latitude and longitude arrays
# _cache_latlon.clear()
return FieldList([field
for x in um
for field in x.fields
if field])
#--- End: def
def _atmosphere_hybrid_sigma_pressure_coordinate(f):
# atmosphere_hybrid_sigma_pressure_coordinate
real_hdr = f.real_hdr
BLEV, BRLEV, BHLEV, BHRLEV = real_hdr[blev:bhrlev+1]
BRSVD1, BRSVD2 = real_hdr[brsvd1:brsvd2+1]
if 'z' not in pmaxes:
indices = [0] * pmndim
indices[pmaxes.index('z')] = slice(1, None, None)
for rec in var.recs[tuple(indices)]:
BLEV, BRLEV, BHLEV, BHRLEV = rec.real_hdr[blev:bhrlev+1]
BRSVD1, BRSVD2 = rec.real_hdr[brsvd1:brsvd2+1]
array.append(BLEV + BHLEV/_pstar)
bounds.append([BRLEV + BHRLEV/_pstar, BRSVD1 + BRSVD2/_pstar])
ak_array.append(BHLEV)
ak_bounds.append([BHRLEV, BRSVD2])
bk_array.append(BLEV)
bk_bounds.append([BRLEV , BRSVD1])
array = numpy_array(array , dtype=float)
bounds = numpy_array(bounds , dtype=float)
ak_array = numpy_array(ak_array , dtype=float)
ak_bounds = numpy_array(ak_bounds, dtype=float)
bk_array = numpy_array(bk_array , dtype=float)
bk_bounds = numpy_array(bk_bounds, dtype=float)
domain = f.field.domain
coord = _create_Coordinate(domain, vdim, axis_code=axis_code,
p=p,
array=array,
bounds_array=bounds,
dimensions=[vdim])
coord = _create_Coordinate(
domain, aux, axis_code=None,
p=p,
pubattr={'standard_name':
'atmosphere_hybrid_sigma_pressure_coordinate_ak'},
units=_units['Pa'],
array=ak_array,
bounds_array=ak_array,
dimensions=[vdim],
aux=True)
coord = _create_Coordinate(
domain, aux, axis_code=None,
p=p,
pubattr={'standard_name':
'atmosphere_hybrid_sigma_pressure_coordinate_bk'},
units=_units['1'],
array=bk_array,
bounds_array=bk_array,
dimensions=[vdim],
aux=True)
else:
cache_key = ('atmosphere_hybrid_sigma_pressure_coordinate',
BLEV, BHLEV, BRLEV, BHRLEV, BRSVD1, BRSVD2)
cache_key_ak = ('atmosphere_hybrid_sigma_pressure_coordinate_ak',
BLEV, BHLEV, BRLEV, BHRLEV, BRSVD1, BRSVD2)
cache_key_bk = ('atmosphere_hybrid_sigma_pressure_coordinate_bk',
BLEV, BHLEV, BRLEV, BHRLEV, BRSVD1, BRSVD2)
if cache_key in _cached_coordinate:
c = _cached_coordinate[cache_key]
domain.insert_dim(c, key=vdim, copy=True)
c = _cached_coordinate[cache_key_ak]
domain.insert_aux(c, axes=[vdim], copy=True)
c = _cached_coordinate[cache_key_bk]
domain.insert_aux(c, axes=[vdim], copy=True)
else:
array = numpy_array((BLEV + BHLEV/_pstar,), dtype=float)
bounds = numpy_array(((BRLEV + BHRLEV/_pstar,
BRSVD1 + BRSVD2/_pstar)), dtype=float)
ak_array = numpy_array((BHLEV,) , dtype=float)
ak_bounds = numpy_array(((BHRLEV, BRSVD2)), dtype=float)
bk_array = numpy_array((BLEV,) , dtype=float)
bk_bounds = numpy_array(((BRLEV, BRSVD1)), dtype=float)
coord = _create_Coordinate(domain, vdim, axis_code=axis_code,
p=p,
array=array,
bounds_array=bounds,
dimensions=[vdim],
cache_key=cache_key)
coord = _create_Coordinate(
domain, aux, axis_code=None,
p=p,
pubattr={'standard_name':
'atmosphere_hybrid_sigma_pressure_coordinate_ak'},
units=_units['Pa'],
array=ak_array,
bounds_array=ak_array,
dimensions=[vdim],
aux=True,
cache_key=cache_key_ak)
coord = _create_Coordinate(
domain, aux, axis_code=None,
p=p,
pubattr={'standard_name':
'atmosphere_hybrid_sigma_pressure_coordinate_bk'},
units=_units['1'],
array=bk_array,
bounds_array=bk_array,
dimensions=[vdim],
aux=True,
cache_key=cache_key_bk)
#--- End: def
def is_um_file(filename):
'''Return True if a file is a PP file or UM fields file.
Note that the file type is determined by inspecting the file's
contents and any file suffix is not not considered.
:Parameters:
filename : str
:Returns:
out : bool
:Examples:
>>> is_um_file('myfile.pp')
True
>>> is_um_file('myfile.nc')
False
>>> is_um_file('myfile.pdf')
False
>>> is_um_file('myfile.txt')
False
'''
try:
f = _open_um_file(filename)
except:
return False
try:
f.close_fd()
except:
pass
return True
#--- End: def
'''
Problems:
Z and P coordinates
/home/david/data/pp/aaaao/aaaaoa.pmh8dec.03328.pp
/net/jasmin/chestnut/data-24/david/testpp/026000000000c.fc0607.000128.0000.00.04.0260.0020.1491.12.01.00.00.pp
skipping variable stash code=0, 0, 0 because: grid code not supported
umfile: error condition detected in routine list_copy_to_ptr_array
umfile: error condition detected in routine process_vars
umfile: error condition detected in routine file_parse
OK 2015-04-01
/net/jasmin/chestnut/data-24/david/testpp/026000000000c.fc0619.000128.0000.00.04.0260.0020.1491.12.01.00.00.pp
skipping variable stash code=0, 0, 0 because: grid code not supported
umfile: error condition detected in routine list_copy_to_ptr_array
umfile: error condition detected in routine process_vars
umfile: error condition detected in routine file_parse
OK 2015-04-01
/net/jasmin/chestnut/data-24/david/testpp/lbcode_10423.pp
skipping variable stash code=0, 0, 0 because: grid code not supported
umfile: error condition detected in routine list_copy_to_ptr_array
umfile: error condition detected in routine process_vars
umfile: error condition detected in routine file_parse
OK 2015-04-01
/net/jasmin/chestnut/data-24/david/testpp/lbcode_11323.pp
skipping variable stash code=0, 0, 0 because: grid code not supported
umfile: error condition detected in routine list_copy_to_ptr_array
umfile: error condition detected in routine process_vars
umfile: error condition detected in routine file_parse
OK 2015-04-01
EXTRA_DATA:
/net/jasmin/chestnut/data-24/david/testpp/ajnjgo.pmm1feb.pp
SLOW: (Not any more! 2015-04-01)
/net/jasmin/chestnut/data-24/david/testpp/xgdria.pdk949a.pp
/net/jasmin/chestnut/data-24/david/testpp/xhbmaa.pm27sep.pp
RUN LENGTH ENCODED dump (not fields file)
/home/david/data/um/xhlska.dak69h0
Field 115 (stash code 9)
dch@eslogin008:/nerc/n02/n02/dch> ff2pp xgvwko.piw96b0 xgvwko.piw96b0.pp
file xgvwko.piw96b0 is a byte swapped 64 bit ieee um file
'''
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