PseudoNetCDF.cmaqfiles package

Submodules

PseudoNetCDF.cmaqfiles.boxmodel module

PseudoNetCDF.cmaqfiles.boxmodel.box_model_conc(conc_path, start_datetime)

PseudoNetCDF.cmaqfiles.boxmodel.box_model_mrg(conc_path, irr_path, start_datetime)

PseudoNetCDF.cmaqfiles.pa module

PseudoNetCDF.cmaqfiles.pa.mrgidx(ipr_paths, irr_paths, idx)

PseudoNetCDF.cmaqfiles.profile module

class PseudoNetCDF.cmaqfiles.profile.bcon_profile(*args, **kwds)

Bases: ioapi_base

toPerim(ncols, nrows, nsteps=1)

toPerimFile(ioapifile)

Parameters:

ioapifile (file with IOAPI metadata)

class PseudoNetCDF.cmaqfiles.profile.icon_profile(*args, **kwds)

Bases: ioapi_base

toGrid(ncols, nrows, nsteps=1)

Parameters:

• ncols (number of ncols for output file)

• nrows (number of rows for output file)

• nsteps (number of output time steps)

toGriddedFile(ioapifile)

Parameters:

ioapifile (file with IOAPI metadata)

Module contents

cmaqfile – CMAQ File Interfaces

class PseudoNetCDF.cmaqfiles.bcon_profile(*args, **kwds)

Bases: ioapi_base

toPerim(ncols, nrows, nsteps=1)

toPerimFile(ioapifile)

Parameters:

ioapifile (file with IOAPI metadata)

PseudoNetCDF.cmaqfiles.box_model_conc(conc_path, start_datetime)

PseudoNetCDF.cmaqfiles.box_model_mrg(conc_path, irr_path, start_datetime)

class PseudoNetCDF.cmaqfiles.cmaqomidat(*args, **kwds)

Bases: PseudoNetCDFFile

Parameters:

path (str) – path to CMAQ-ready OMI file. This is the output of create_omi preprocessor. See notes for general form.

Notes

File has the genearl form

nlat 17 nlon 17 yeardate latitude 180Z 157.5W … 1990.203 80 426 415 … … 1990.203 -80 260 253 …

class PseudoNetCDF.cmaqfiles.griddesc(*args, **kwds)

Bases: ioapi_base

griddesc is designed to read IOAPI griddesc files and create a file with basic CF metadata. An example format of GRIDDESC is show below with two grids on one projection.

‘ ‘ ‘LCC’

2 33.000 45.000 -97.000 -97.000 40.000

‘ ‘ ‘SE52BENCH’ ‘LCC’ 792000.000 -1080000.000 12000.000 12000.000 100 80 1 ‘36US3’ ‘LCC’ -2952000.000 -2772000.000 36000.000 36000.000 172 148 1 ‘ ‘

Parameters:

• path (str or file-like) – If path is has a read method, it will be used directly. If path is a path to a file on disk, it will be read. If none of these, treat the path as text content. If path is None, load a griddesc using properties provided.

• GDNAM (str) – Name the grid to be used. If not provided, the first will be used

• VGLVLS (tuple) – Iterable of layer edge (k+1) values for the vertical grid.

• VGTOP (float) – Top of vertical grid.

• VGTYP (int) – Determines the units of VGLVLS and VGTOP. (7: WRF sigma-p, 6: meters asl, for more details see IOAPI documentation)

• SDATE (int) – Starting julian date (YYYYJJJ) or -635

• STIME (int) – Starting time as HHMMSS

• TSTEP (int) – IOAPI time step in HHMMSS

• FTYPE (int) – 1 for gridded; 2 for boundary

• var_kwds (tuple, list, or dict) – See setdefvars; Defaults to {‘DUMMY’: {‘units’: ‘unknown’}}

• nsteps (int) – Number of time steps to use. Should be coupled with SDATE, STIME, and TSTEP. nsteps > 1 is not compatible with time independent (TSTEP=0) or SDATE=-635

• withcf (bool) – If true, then CF compatible variables that describe dimensions and time are added.

• prop_kw (mappable) – Can provide additional IOAPI (or other) properties for the file.

adddims(withcf=True)

Add spatial dimensions

Parameters:

withcf (bool) – If true, add Climate and Forecasting convention variables

Return type:

None

addtime(nsteps=1)

Adds TFLAG variable

Parameters:

nsteps (int) – Number of time steps to add

Return type:

None

setdefvars(var_kwds)

Parameters:

var_kwds (list, tuple, or dictionary) – Variables with units or just a list of variables

setgrid(key=None, withcf=True)

Remakes the file to use the grid specified by key

Parameters:

• key (str) – GDNAM to set the grid of the file

• withcf (bool) – Passed to adddims

Return type:

None

class PseudoNetCDF.cmaqfiles.icon_profile(*args, **kwds)

Bases: ioapi_base

toGrid(ncols, nrows, nsteps=1)

Parameters:

• ncols (number of ncols for output file)

• nrows (number of rows for output file)

• nsteps (number of output time steps)

toGriddedFile(ioapifile)

Parameters:

ioapifile (file with IOAPI metadata)

class PseudoNetCDF.cmaqfiles.ioapi(*args, **kwds)

Bases: ioapi_base, netcdf

createDimension(*args, **kwds)

Create a dimension

Parameters:

• name (string) – name for dimension

• length (integer) – maximum length of dimension

Returns:

dim – new dimension

Return type:

PseudoNetCDFDimensions

createVariable(*args, **kwds)

Wrapper on PseudoNetCDF.createVariable that updates VAR-LIST, NVARS, VAR, and TFLAG. Also adds long_name, var_desc, and units if not already in properties. long_name and var_desc default to name, while units defaults to unknown. These properties will also be adjusted to expected lengths (16, 80, 16).

See also

see

classmethod from_arrays(*args, **kwds)

Thin wrapper around ioapi_base.from_arrays

classmethod from_ncf(infile)

Parameters:

infile (PseudoNetCDF-like file)

Returns:

outf

Return type:

PseudoNetcdf-like file

classmethod isMine(*args, **kwds)

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.

class PseudoNetCDF.cmaqfiles.ioapi_base(*args, **kwds)

Bases: PseudoNetCDFFile

apply(*args, **kwds)

Wrapper PseudoNetCDFFile.applyAlongDimensions that corrects ROW, COL, LAY and TIME meta-data according to the ioapi format

Parameters:

PseudoNetCDFFile.applyAlongDimensions (see)

applyAlongDimensions(*args, **kwds)

Wrapper PseudoNetCDFFile.applyAlongDimensions that corrects ROW, COL, LAY and TIME meta-data according to the ioapi format

Parameters:

PseudoNetCDFFile.applyAlongDimensions (see)

audit_meta(fail='warn')

Audit the IOAPI metadata. Checks existence of properties, dimensions internal consistency of properties and dimensions, and character lengths

Parameters:

fail (bool) – If fail, ‘warn’ or ‘error’ or ‘ignore’

Returns:

audit stats and audit checklist dictionaries

Return type:

passing, audit, var_audit

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)

Wrapper on PseudoNetCDF.copyVariable that updates VAR-LIST, NVARS, VAR, and TFLAG

See also

see

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

Wrapper on PseudoNetCDF.createVariable that updates VAR-LIST, NVARS, VAR, and TFLAG. Also adds long_name, var_desc, and units if not already in properties. long_name and var_desc default to name, while units defaults to unknown. These properties will also be adjusted to expected lengths (16, 80, 16).

See also

see

eval(*args, **kwds)

Wrapper PseudoNetCDFFile.eval that corrects VAR-LIST and TFLAG meta-data according to the ioapi format

Parameters:

PseudoNetCDFFile.eval (see)

classmethod from_arrays(dims=None, attrs=None, nameattr='long_name', fileattrs=None, **inarrkw)

Create a new ioapi file from arrays.

Parameters:

• dims (iterable) – Explicit dimensions. If not provided, they will be diagnosed: TFLAG: (‘TSTEP’, ‘VAR’, ‘DATE-TIME’) Other 4D: (‘TSTEP’, ‘LAY’, ‘ROW’, ‘COL’) Other 3D: (‘TSTEP’, ‘LAY’, ‘PERIM’) Other 2D: (‘ROW’, ‘COL’)

• attrs (mappable) – Attributes for all variables (e.g., units). long_name and var_desc will be set based on key if not provided.

• nameattr (str)

• fileattrs (mappable) – Attributes for the file to be created.

• inarrkw (mappable) – Keys are the names of variables to be created and the value should be an array of values.

Returns:

outf

Return type:

PseudoNetcdf-like file

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

Wrapper PseudoNetCDFFile.getMap that uses NCOLS, XCELL NROWS, and YCELL to calculate map bounds if basemap_auto

Parameters:

PseudoNetCDFFile.getMap (see)

getVarlist(update=True, prune=True, retval='list')

Returns:

• update (boolean) – update files attributes to be consistent

• prune (bool) – If True, remove variables that are missing or have names longer than 16 characters

• retval (str) – Return formatted string ‘str’ or list otherwise

Notes

If VAR-LIST does not exist, it is added assuming all variables with dimensions (‘TSTEP’, ‘LAY’, …) are variables

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

Parameters:

• vglvls (iterable) – the new vglvls (edges)

• vgtop (scalar) – Converting to new vgtop

• interptype (string) – ‘linear’ uses a linear interpolation ‘conserve’ uses a mass conserving interpolation

• extrapolate (boolean) – allow extrapolation beyond bounds with linear, default False

• fill_value (boolean) – set fill value (e.g, nan) to prevent extrapolation or edge continuation

Returns:

outf – PseudoNetCDFFile with all variables interpolated

Return type:

ioapi_base

Notes

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

classmethod isMine(path, *args, **kwds)

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.

mask(*args, **kwds)

Wrapper on PseudoNetCDFFile.subsetVariables that updates VAR-LIST, NVARS, VAR, and TFLAG

See also

see

plot(varkey, plottype=None, ax_kw=None, plot_kw=None, cbar_kw=None, map_kw=None, dimreduction='mean')

Parameters:

• varkey (string) – the variable to plot

• plottype (string) – longitude-latitude, latitude-pressure, longitude-pressure, vertical-profile, time-longitude, time-latitude, time-pressure, default, last two dimensions in reverse order

• ax_kw (dictionary) – keywords for the axes to be created

• plot_kw (dictionary) – keywords for the plot (plot, scatter, or pcolormesh) to be created

• cbar_kw (dictionary or bool or None) – keywords for the colorbar; if True or None, use defaults. If False, do not create a colorbar

• map_kw (dictionary or bool or None) – keywords for the getMap routine, which is only used with map capable dimensions (ie, plottype=’longitude-latitude’) If True or None, use default configuration dict(countries=True, coastlines=True, states=False, counties=False). If False, do not draw a map.

• dimreduction (string or function) – dimensions not being used in the plot are removed using applyAlongDimensions(dimkey=dimreduction) where each dimenions.

setncatts(attdict)

Wrapper on PseudoNetCDF.setncatts that updates WDATE, and WTIME

See also

see

slice(*args, **kwds)

Wrapper PseudoNetCDFFile.sliceDimensions that corrects ROW, COL, LAY and TIME meta-data according to the ioapi format

Parameters:

PseudoNetCDFFile.sliceDimensions (see)

sliceDimensions(*args, **kwds)

Wrapper PseudoNetCDFFile.sliceDimensions that corrects ROW, COL, LAY and TIME meta-data according to the ioapi format

Parameters:

PseudoNetCDFFile.sliceDimensions (see)

subset(varkeys, inplace=False, exclude=False, keepcoords=True)

Wrapper on PseudoNetCDFFile.subsetVariables that updates VAR-LIST, NVARS, VAR, and TFLAG

See also

see

subsetVariables(varkeys, inplace=False, exclude=False, keepcoords=True)

Wrapper on PseudoNetCDFFile.subsetVariables that updates VAR-LIST, NVARS, VAR, and TFLAG

See also

see

updatemeta(attdict={}, sortmeta=False)

Parameters:

• attdict (dictionary) – key value pairs to update meta data

• sortmeta (boolean) – sort meta data after update

Return type:

None

Notes

Meta data not provided or present will be inferred or made up. (See _ioapi_defaults)

updatetflag(overwrite=None, startdate=None, tstep=None)

class PseudoNetCDF.cmaqfiles.jtable(*args, **kwds)

Bases: PseudoNetCDFFile

interpj(key_or_var, lay, lat, angle)