GEOS-Chem¶

class PseudoNetCDF.geoschemfiles.bpch(*args, **kwds)[source]¶

bpch_path: path to binary punch file tracerinfo: path to ascii file with tracer definitions diaginfo: path to ascii file with diagnostic group definitions mode : {‘r+’, ‘r’, ‘w+’, ‘c’}, optional

The file is opened in this mode:

+——+———————————————————–+

| ‘r’ | Open existing file for reading only. |

+——+———————————————————–+

| ‘r+’ | Open existing file for reading and writing. |

+——+———————————————————–+

| ‘w+’ | Create or overwrite existing file for reading and writing.|

+——+———————————————————–+

| ‘c’ | Copy-on-write: assignments affect data in memory, but |

| | changes are not saved to disk. The file on disk is |

| | read-only. |

+——+———————————————————–+

timeslice: If the file is larger than 2GB, timeslice provides a way
to subset results. The subset requested depends on the data type of timeslice:

int: return the a part of the file if it was broken
into 2GB chunks (0..N-1)

slice: return the times that correspond to that slice
(i.e., range(ntimes)[timeslice])

list/tuple/set: return specified times where each
time is in the set (0..N-1)

noscale: Do not apply scaling factors vertgrid: vertical coordinate system (options: ‘GEOS-5-REDUCED’,

‘GEOS-5-NATIVE’, ‘MERRA-REDUCED’, ‘MERRA-NATIVE’, ‘GEOS-4-REDUCED’, ‘GEOS-4-NATIVE’, default ‘GEOS-5-REDUCED’)

nogroup: False - use all groups, True - use no groups, list of groups
to ignore

apply(verbose=0, **dimfuncs)¶

Similar to numpy.apply_along_axis, but for damed dimensions and processes dimensions as well as variables

Parameters

dimfuncs (dictionary) – key value pairs where the key is a dimensions and the value is a 1D function (func1d) or a dictionary. If the value is a dictionary it must include func1d as a function and any keyword arguments as additional options
verbose (integer) – 0 silent, 1 show variable, 2 show dimensions and variables

Returns

outf – instance with variables and dimensions after processing

Return type

PseudoNetCDFFile

applyAlongDimensions(verbose=0, **dimfuncs)¶

Similar to numpy.apply_along_axis, but for damed dimensions and processes dimensions as well as variables

Parameters

dimfuncs (dictionary) – key value pairs where the key is a dimensions and the value is a 1D function (func1d) or a dictionary. If the value is a dictionary it must include func1d as a function and any keyword arguments as additional options
verbose (integer) – 0 silent, 1 show variable, 2 show dimensions and variables

Returns

outf – instance with variables and dimensions after processing

Return type

PseudoNetCDFFile

close()¶: Does nothing. Implemented for continuity with Scientific.IO.NetCDF

copy(props=True, dimensions=True, variables=True, data=True)¶

Function for making copies of the same type

Parameters

props (boolean) – include properties (default: True)
dimensions (boolean) – include dimensions (default: True)
variables (boolean) – include variable structures (default: True)
data (boolean) – include variable data (default: True)

Returns

outf

Return type

PseudoNetCDFFile instance

copyVariable(var, key=None, dtype=None, dimensions=None, fill_value=None, withdata=True)¶

Copy var into self as vark

Parameters

var (PseudoNetCDFVariable) – netCDF4.Variable-like object (must have ncattrs and setncatts)
key (string) – key for variable in self (can be omitted if var has name, standard_name, or long_name)
dtype (string or numpy.dtype) – change the data type to dtype
dimensions (iterable of strings) – change the dimensions to dimensions
fill_value (integer or flaot) – change the fill_value to this values
withdata (boolean) – default True, copies data

Returns

myvar – copy of var in this file

Return type

PseuodNetCDFVairable

createDimension(name, length)¶

Create a dimension

Parameters

name (string) – name for dimension
length (integer) – maximum length of dimension

Returns

dim – new dimension

Return type

PseudoNetCDFDimensions

createVariable(name, type, dimensions, fill_value=None, **properties)¶

Create a variable

Parameters

name (string) – name for new variable
type (string or numpy dtype) – code (e.g., ‘f’, ‘i’, ‘d’)
dimensions (tuple of strigns) – dimension keys that can be found in objects’ dimensions dictionary

Returns

var

Return type

new variable

date2num(time, timekey='time')¶

Parameters

time (array-like) – array of datetime.datetime objects
timekey (str) – time variable key which requires units and should have calendar. If calendar is missing, standard is the default. default ‘time’

Returns

num – time in relative time as defined by units of time variable (i.e., timekey) which defaults to ‘time’

Return type

array-like

eval(expr, inplace=False, copyall=False)¶

Evaluate expr and return a PseudoNetCDFFile object with resutl

Parameters

expr (string) – expression to evaluate
inplace (boolean) – create the new variable in this netcdf file (default False)
copyall (boolean) – if not inplace, should all variables be copied to new file

Returns

outf – instance with renamed variable (this file if inplace = True)

Return type

PseudoNetCDFFile

flush()¶: Does nothing. Implemented for continuity with Scientific.IO.NetCDF

classmethod from_ncf(infile)¶

Parameters: infile (PseudoNetCDF-like file) –
Returns: outf
Return type: PseudoNetcdf-like file

classmethod from_ncvs(*invars, **invarkw)¶

Parameters

invars (list) – NetCDF-like variable must have standard_name, long_name or name
invarkw (kwds) – NetCDF-like variables

Returns

outf

Return type

PseudoNetcdf-like file

getCoords()¶: Return a list of coordkeys

getMap(maptype='basemap_auto', **kwds)¶

Description

Parameters

maptype (string) –
choices ‘basemap’, ‘basemap_auto’, ‘cartopy’ (not yet) basemap : attempts to open a basemap with only supplied kwds basemap_auto : automatically adds llcrnrlon,llcrnrlat,u

rcrnrlon,urcrnrlat based on longitude_bounds
**kwds (keywords) – for basemap or cartopy

Returns

map

Return type

basemap or cartopy axis

getTimes(bounds=False)¶

Get an array of datetime objects

Parameters

datetype (string or numpy.dtype) – ‘datetime’ or datetime64 dtype
bounds (boolean) – get time boundaries

Returns

out – datetime objects or array of numpy’s datetype type

Return type

array

Notes

self must have a time or TFLAG variable

get_dest()¶

Returns: path – path where a new file is created on some action
Return type: str

Notes

If None, a file is created in memory. Else, a netcdf file is created on disk.

get_varopt()¶

Get options

Parameters: None –
Returns: options
Return type: dictionary of options

getncatts()¶

Return all ncattrs keys and values as a dictionary

Returns: attdict – key/value pairs of properties
Return type: dictionary

getproj(withgrid=False, projformat='pyproj')¶

Description

Parameters

withgrid (boolean) – use grid units instead of meters
projformat (string) – ‘pyproj’ (default), ‘proj4’ or ‘wkt’ allows function to return a pyproj projection object or a string in the format of proj4 or WKT

Returns

proj – (wkt, proj4) or pyprojProj (pyproj)

Return type

string pyproj.Proj

ij2ll(i, j)¶: i, j to center lon, lat

insertDimension(newonly=True, multionly=False, before=None, after=None, inplace=False, **newdims)¶

Insert dimensions with keys and lengths from newdims

Parameters

**newdims (dictionary) – where key is the new dimension and value is the length
newonly (boolean) – Only add dimension to variables that do not already have it, default True
multionly (boolean) – Only add dimension if there are already more than one (good for ignoring coordinate dimensions)
before (string) – if variable has this dimension, insert the new dimension before it. Otherwise, add to the beginning. (before takes precedence)
after (string) – if variable has this dimension, insert the new dimension after it. Otherwise, add to the beginning.
inplace (boolean) – create the new variable in this netcdf file (default False)

Returns

outf – instance will new dimension in dimensions and variables

Return type

PseudoNetCDFFile

Notes

Adding a non unity dimension will cause the data to be repeated along the new axis.
If order of addition matters, use multiple calls. newdimsuse will be a non-ordered dictionary

interpDimension(dimkey, newdimvals, coordkey=None, **interpkwds)¶

Parameters

dimkey (string) – the new dimension for interpolation
newdimvals (iterable) – the new values to interpolate to
coordkey (string) – the variable to use as the old coordinate values
interptype (string) –

‘linear’ or ‘conserve’. linear uses a linear interpolation
conserve uses a mass conserving interpolation
extrapolate (boolean) – allow extrapolation beyond bounds with linear, default False
fill_value (numeric value) – set fill value (e.g, nan) to prevent extrapolation or edge continuation

Returns

outf – instance with all variables interpolated

Return type

PseudoNetCDFFile

Notes

When extrapolate is false, the edge values are used for points beyond the inputs.

interpSigma(vglvls, vgtop=None, interptype='linear', extrapolate=False, fill_value='extrapolate', layerdims=None, approach='eta', verbose=0)¶

Parameters

self (the file to interpolate from must have VGLVLS) –
vglvls (the new vglvls (edges)) –
vgtop (Converting to new vgtop (Pascals)) –
interptype ('linear' or 'conserve') – linear : uses a linear interpolation conserve : uses a mass conserving interpolation
extrapolate (allow extrapolation beyond bounds with linear,) – default False
fill_value (set fill value (e.g, nan) to prevent extrapolation or edge) – continuation
layerdims (specify layer dimension, None will apply to all dimensions) – named layer*
approach –

etause simple eta coordinates to calculate sigma and
interpolate

pressure : requires surface pressure
verbose (0-inf show more) –

Returns

Return type

outf - ioapi_base PseudoNetCDFFile with al variables interpolated

Notes

When extrapolate is false, the edge values are used for points beyond the inputs.

classmethod isMine(*args, **kwds)[source]¶: True if this file or object can be identified for use by this class. Useful to override for classes that can be initialized from disk.

ll2ij(lon, lat, bounds='error')¶

Converts lon/lat to 0-based indicies (0,M), (0,N)

Parameters

lon (scalar or iterable of longitudes in decimal degrees) –
lat (scalar or iterable of latitudes in decimal degrees) –
bounds (ignore, error, warn if i,j are out of domain) –

Returns

i, j

Return type

indices (0-based) for variables

ll2xy(lon, lat)¶: lon and lat are converted to local lon and lat (-180,180) (-90, 90)

mask(where=None, less=None, less_equal=None, greater=None, greater_equal=None, values=None, equal=None, invalid=False, mask=None, dims=None, fill_value=- 999, coords=False, verbose=0)¶

Apply mask to all variables of same shape or just where dimensions match.

Parameters

where (array-like) – boolean array to use as a mask see numpy.ma.masked_where
greater (scalar) – mask when values are greater than this value see numpy.ma.masked_greater
less (scalar) – mask when values are less than this value see numpy.ma.masked_less
greater_equal (scalar) – mask when values are greater than or equal to this value see numpy.ma.masked_greater
less_equal (scalar) – mask when values are less than or equal to this value see numpy.ma.masked_less
values (scalar) – mask when values are equal to this value within standard floating point see numpy.ma.masked_values
equal (scalar) – mask when values are exactly this value (i.e., integers) see numpy.ma.masked_equal
invalid (boolean) – mask when values are invalid, see numpy.ma.masked_invalid
mask (array-like) – alias for where
dims (iterable of strings) – only apply “mask” or “where” to variables with these dimensions no effet on other masks
fill_value (scalar) – value to use as the fill_value for new arrays
coords (boolean) – if True, apply masks to coordinate variables. Default, False
verbose (int) – level of verbosity for function, mostly for debugging

Returns

outf – instance with masked variables

Return type

PseudoNetCDFFile