aqmbc package

Subpackages

Submodules

aqmbc.bcon module

aqmbc.bcon.bc(inpath, outpath, metaf, tslice=None, vmethod='conserve', exprpaths=None, clobber=False, dimkeys=None, format_kw=None, history='', speedup=None, timeindependent=False, verbose=1, minvalue=None)[source]
Parameters:

  • inpath (str) – path to input file

  • outpath (str) – path to output file

  • metaf (netcdf-like) – Metadata file (CRO for ICON, BDY for BCON)

  • tslice (slice) – Optional time slice (e.g., slice(0) for ICON)

  • vmethod (str) – method to use for vertical interpolation (conserve or linear)

  • exprpaths (list) – text files with species translations

  • clobber (bool) – overwrite existing files

  • speedup (bool) – slice file to load into memory. More mem, but faster

  • timeindependent (bool) – If True and input has just 1 time, write out as an IOAPI time-independent file.

  • minvalue (scalar) – Passed to translate

Return type:

None

Notes

  • Saves BCON or ICON to file.

  • Operations:

    1. window

    2. horizontal extraction

    3. vertical interpolation

    4. species translation

aqmbc.bcon.dimparser(dimstr)[source]
Parameters:

dimstr (str) – key=value pairs delimited by commas

Returns:

out – mapping table between IOAPI gridded and input dimensions

Return type:

dict

aqmbc.bcon.formatparser(fmtstr)[source]
Parameters:

fmtstr (str) – string with format and option key value pairs delimited by commas option key value pairs should be in a format consistent with dict call dict(key1=val1, key2=val2, …)

Returns:

out – format=first word otherkeys=key value pairs delimited by commas

Return type:

dict

aqmbc.bcon.ijslice(infile, metaf, i, j, dimkeys, verbose=1)[source]
Parameters:

  • infile (netcdf-like) – input file

  • metafile (netcdf-like) – file with longitude and latitude

Returns:

bconf

Return type:

file at metaf

aqmbc.bcon.kinterp(infile, metaf, vmethod, verbose=1)[source]
Parameters:

  • infile (netcdf-like) – input file

  • metaf (netcdf-like) – file with longitude and latitude

  • vmethod (str) – method for vertical inteprolation (conserve or linear)

Returns:

bconvf

Return type:

file at new vertical levels

aqmbc.bcon.saveioapi(inf, outf, outpath, metaf, dimkeys, timeindependent=False, verbose=1)[source]
Parameters:

  • inf (netcdf-like file) – Must support getTimes method

  • outf (netcdf-like file) – file for output

  • metaf (netcdf-like file) – metadata file

  • dimkeys (dict) – translation dictionary for dimensions

  • timeindependent (bool) – If True and number of times is 1, the file will be stored as IOAPI time-independent

  • Results –

  • ------- –

  • out (netcdf-like file) – file that was output

aqmbc.bcon.translate(infile, exprpaths, verbose=1)[source]
Parameters:

  • infile (netcdf-like) – File input

  • exprpaths (list) – paths to expr file

Returns:

outf

Return type:

file output

aqmbc.bcon.wndw(varfile, metaf, dimkeys, tslice, speedup=None, verbose=1)[source]
Parameters:

  • varfile (netcdf-like) – input file

  • metafile (netcdf-like) – file with longitude and latitude

Returns:

  • wndwf (file windows in lon/lat space)

  • i (indices for wndwf at metaf)

  • j (indices for wndwf at metaf)

aqmbc.cmaq module

aqmbc.cmaq.cmaqready(date, inpaths, outpath=None, verbose=0, minvalue=1e-30)[source]

Concatenate inpaths on time and then interpolate to 25h instantaneous times for CMAQ. Also trims FILEDESC and HISTORY if they are too long.

Parameters:

  • date (date-like or string) – Date for CMAQ-ready file.

  • inpaths (list or str) – List of paths to use as the source or template to find inputs

  • outpath (str or None) – If None, return the file. Otherwise, write it out and return the path

  • verbose (int) – Level of verbosity

  • minvalue (scalar) – Minimum value

Returns:

outpath – Output file or path.

Return type:

str or dataset

aqmbc.exprlib module

aqmbc.exprlib.gc12

options for GEOS-Chem version 12 for CB6r3 with AE7 aerosols

Type:

tuple

aqmbc.exprlib.gc12_soas

same as above, but for the Simple SOA option.

Type:

tuple

aqmbc.exprlib.gc14

options for GEOS-Chem version 14 with CB6r5 with AE7 aerosols

Type:

tuple

aqmbc.exprlib.gc14_soas

same as above, but for the simple SOA option.

Type:

tuple

aqmbc.exprlib.raqms

cb6r4 and ae6 definitions for RAQMS

Type:

tuple

aqmbc.options module

aqmbc.options.getmetaf(bctype='bcon', gdnam='12US1', vgnam='EPA_35L', gdpath=None)[source]
bctypestr

bcon (boundary) or icon (initial) boundary conditions.

gdnamstr

Name of grid in gdpath

vgnamstr

Name of vertical grid (must exist in vglvls)

gdpathstr or None

If none, looks for GRIDDESC environment, then looks for a local file, then uses the default.

aqmbc.report module

aqmbc.report.barplot(ds, bar_kw=None)[source]
Parameters:

  • ds (pandas.Series) – Series get from makestats or getstats

  • bar_kw (mappable) – Options for the barplot function (including ax)

Returns:

ax – Axes object with barplot

Return type:

matplotlib.axes.Axes

aqmbc.report.get_vertprof(inbcon, varkeys=None, func='mean', verbose=0, outpath=None)[source]
Parameters:

  • inbcon (list or str) –

    If str, inbcon = sorted(glob.glob(inbcon)) If list, items should be str or xarray.Dataset object.

    If str, infiles = [xr.open_dataset(inpath) for inpath in inbcon] If Datasets, infiles = inbcon

  • varkeys (list or None) – variable keys (if None, use all)

  • func (str) – Name of function to apply to each variable (min, mean, max, median)

  • verbose (int) – Level of verbosity

  • outpath (str or None) – Path to save (or retrieve) the vertical profile from

Returns:

vf – Variables have func applied to all dimensions except for LAY.

Return type:

xarray.Dataset

aqmbc.report.getstats(inbcon, varkeys=None, verbose=0, add_summary=True, outpath=None, draft=False)[source]
Parameters:

  • inbcon (list or str) –

    If str, inbcon = sorted(glob.glob(inbcon)) If list, items should be str or xarray.Dataset object.

    If str, infiles = [xr.open_dataset(inpath) for inpath in inbcon] If Datasets, infiles = inbcon

    If outpath is not None, inbcon must be a str or list of paths

  • varkeys (list) – List of variable keys to process

  • verbose (int) – Level of verbosity

  • add_summary (bool) – Add summary level data

  • outpath (str or None) – Path to save (or retrieve) results from. Cached results will only be used if the outpath file is newer than all the inputs.

  • draft (bool) – If True, use actual_range and actual_median properties instead of file data.

Returns:

statdf – Dataframe with rows for each file and variable combination. Each row has min, mean, median, max, std

Return type:

pandas.DataFrame

aqmbc.report.make_vertprof(inbcon, varkeys=None, func='mean', verbose=0)[source]
Parameters:

  • inbcon (list or str) –

    If str, inbcon = sorted(glob.glob(inbcon)) If list, items should be str or xarray.Dataset object.

    If str, infiles = [xr.open_dataset(inpath) for inpath in inbcon] If Datasets, infiles = inbcon

  • varkeys (list or None) – variable keys (if None, use all)

  • func (str) – Name of function to apply to each variable (min, mean, max, median)

  • verbose (int) – Level of verbosity

Returns:

vf – Variables have func applied to all dimensions except for LAY.

Return type:

xarray.Dataset

aqmbc.report.makestats(inbcon, varkeys=None, verbose=0, draft=False)[source]
Parameters:

  • inbcon (list or str) –

    If str, inbcon = sorted(glob.glob(inbcon)) If list, items should be str or xarray.Dataset object.

    If str, infiles = [xr.open_dataset(inpath) for inpath in inbcon] If Datasets, infiles = inbcon

  • varkeys (list) – List of variable keys to process

  • verbose (int) – Level of verbosity

  • draft (bool) – If True, use actual_range and actual_median properties instead of file data.

Returns:

statdf – Dataframe with rows for each file and variable combination. Each row has min, mean, median, max, std

Return type:

pandas.DataFrame

aqmbc.report.plot_2spc_vprof(vprof, vminprof=None, vmaxprof=None, v1k='O3', v2k=None)[source]
aqmbc.report.plot_gaspm_bars(statdf, filekey='Overall', metric='median', sortmetric='median')[source]
aqmbc.report.plot_vprof(vmean, vmin=None, vmax=None, ax=None, **kwds)[source]
Parameters:

  • vmean (xarray.DataArray) – Average of vertical profile at time steps; must have the TSTEP and LAY dimensions

  • vmin (xarray.DataArray) – Optional lower and upper bounds

  • vmax (xarray.DataArray) – Optional lower and upper bounds

  • ax (matplotlit.axes.Axes) – Optional axes to add lines to.

  • kwds (mappable) – Properties for lines

Returns:

ax – If ax was provided, the same ax is returned. Otherwise, a new ax is created using subplots.

Return type:

matplotlit.axes.Axes

aqmbc.report.reportfromcfg(cfgobjs, cfgtype='path')[source]

Runs getstats, and get_vertprof and save to disk If summaryfigs=’y’, run plot_gaspm_bars and plot_2spc_vprof and save results to disk.

Parameters:

  • cfgobjs (list) – List of paths, files, or dictionaries

  • cfgtype (str) – ‘path’, ‘file’, or ‘dict’

Return type:

None

aqmbc.report.summarize(statdf, append=True)[source]
Parameters:

  • statdf (pandas.DataFrame) – DataFrame from makestats or getstats

  • append (bool) – If True, add record to statdf and return full dataframe.

Returns:

statdf – Add Overall record for each variable where mean and std are averages, unit and min are their minimums, max is its maximum, and median is its median.

Return type:

pandas.DataFrame

Module contents

Code for making CMAQ-ready boundary condition files

Contents

bconmodule

module with functions for making boundary condition files

cmaqmodule

module for making files CMAQ ready

reportmodule

module with convenience functions for reporting

defnpathstr

Path to all definition files available in examples.

runcfgfunction

Function to run aqmbc from configuration files

Examples

Ex Python GEOS-Chem

import PseudoNetCDF as pnc import aqmbc

inpath = ‘/path/to/geoschem.nc’ bcpath = ‘BCON.nc’ # using built in expressions exprpaths = [f’{aqmbc.defnpath}/gc/gcnc_airmolden.expr’,

f’{aqmbc.defnpath}/gc/gc14_to_cb6r5.expr’]

metaf = pnc.pncopen(‘/path/to/METCRO3D_ANYDATE’, format=’ioapi’) bc(inpath, bcpath, metaf, vmethod=’linear’, exprpaths=exprpaths,

dimkeys=dict(TSTEP=’time’, LAY=’lev’, ROW=’lat’, COL=’lon’), format_kw=’gcnc’, history=’just a test’)

Ex Scripting

python -m aqmbc -t runfolder cd runfolder # copy a cfg file as run.cfg # edit run.cfg for your application. python -m aqmbc run.cfg

Version History

  • 0.4.1: Update bc and cmaqready to apply a minimum value and allow inpaths

    to be provided by a template. The minimum value (minvalue) can be set in the common configuration section. Also, improved reporting functions and automated reporting via the config file.

  • 0.4.0: Change verbose to string for newer configparser compat

    Update FILEDESC and HISTORY outputs to limit to 60*80 char Added cmaq module with cmaqready to stack, interpolate, and when necessary clean metadata. Added some reporting tools, expression library and examples. Needs better documentation on many objects.

aqmbc.bc(inpath, outpath, metaf, tslice=None, vmethod='conserve', exprpaths=None, clobber=False, dimkeys=None, format_kw=None, history='', speedup=None, timeindependent=False, verbose=1, minvalue=None)[source]
Parameters:

  • inpath (str) – path to input file

  • outpath (str) – path to output file

  • metaf (netcdf-like) – Metadata file (CRO for ICON, BDY for BCON)

  • tslice (slice) – Optional time slice (e.g., slice(0) for ICON)

  • vmethod (str) – method to use for vertical interpolation (conserve or linear)

  • exprpaths (list) – text files with species translations

  • clobber (bool) – overwrite existing files

  • speedup (bool) – slice file to load into memory. More mem, but faster

  • timeindependent (bool) – If True and input has just 1 time, write out as an IOAPI time-independent file.

  • minvalue (scalar) – Passed to translate

Return type:

None

Notes

  • Saves BCON or ICON to file.

  • Operations:

    1. window

    2. horizontal extraction

    3. vertical interpolation

    4. species translation

aqmbc.runcfg(cfgobjs, cfgtype='path', warningfilter='ignore', dryrun=False, speedup=None)[source]
Parameters:

  • cfgobjs (list) – List of paths, files, or dictionaries

  • cfgtype (str) – ‘path’, ‘file’, or ‘dict’

  • warningfilter (str) – str accepted by warnings.simplefilter

  • dryrun (bool) – If True, return config after testing parsing.

  • speedup (bool or None) – If True, use more memory but run faster. If None, heursitcally decide.