In [1]:

    

from notebook.services.config import ConfigManager
cfm = ConfigManager()
cfm.update('livereveal', {
              'theme': 'simple',
              'transition': 'convex',
              'start_slideshow_at': 'selected'
})


    

    
Out[1]:





{'start_slideshow_at': 'selected', 'theme': 'simple', 'transition': 'convex'}

In [2]:

    

# Prepare my slides
%pylab inline
%cd working


    

    




Populating the interactive namespace from numpy and matplotlib
/Users/barronh/Downloads/GCandPython/working

In [3]:

    

%mkdir icartt
!curl -Lo icartt/dc3-mrg60-dc8_merge_20120518_R7_thru20120622.ict http://www-air.larc.nasa.gov/cgi-bin/enzFile?e38EE03EFAE02C04F06E9647DAF98F48D6A2f7075622d6169722f534541433452532d4443332f4d45524745532f315f4d494e5554452e4443385f4d52472f6463332d6d726736302d6463385f6d657267655f32303132303531385f52375f7468727532303132303632322e696374


    

    




mkdir: cannot create directory ‘icartt’: File exists
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 30.5M  100 30.5M    0     0  1227k      0  0:00:25  0:00:25 --:--:-- 1327k

In [4]:

    

!curl -LO ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v10-01/v10-01-public-release/Run0/tracerinfo.dat
!curl -LO ftp.as.harvard.edu/gcgrid/geos-chem/1yr_benchmarks/v10-01/v10-01-public-release/Run0/diaginfo.dat


    

    




  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 83324  100 83324    0     0  47062      0  0:00:01  0:00:01 --:--:-- 47102
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 13840  100 13840    0     0   8686      0  0:00:01  0:00:01 --:--:--  8704

In [5]:

    

import zipfile
zf = zipfile.ZipFile('bpch.zip')
zf.extract('bpch/ctm.bpch.v10-01-public-Run0.2013050100')


    

    
Out[5]:





'/Users/barronh/Downloads/GCandPython/working/bpch/ctm.bpch.v10-01-public-Run0.2013050100'

In [6]:

    

!pncdump.py --header -v Fractional_Day,UTC,O3_ESRL -f ffi1001 icartt/dc3-mrg60-dc8_merge_20120518_R7_thru20120622.ict


    

    




PseudoNetCDF.core._files.PseudoNetCDFFile icartt/dc3-mrg60-dc8_merge_20120518_R7_thru20120622.ict {
dimensions:
        POINTS = 6817 ;

variables:
        double Fractional_Day(POINTS);
                Fractional_Day:units = "Fractional_Day, none" ;
                Fractional_Day:fill_value = -999999.0 ;
                Fractional_Day:llod_value = "N/A" ;
                Fractional_Day:scale = 1.0 ;
                Fractional_Day:llod_flag = -888888 ;
                Fractional_Day:standard_name = "Fractional_Day" ;
                Fractional_Day:ulod_flag = -777777 ;
                Fractional_Day:missing_value = -999999 ;
                Fractional_Day:ulod_value = "N/A" ;
        double O3_ESRL(POINTS);
                O3_ESRL:units = "ppbv" ;
                O3_ESRL:fill_value = -999999.0 ;
                O3_ESRL:llod_value = "N/A" ;
                O3_ESRL:scale = 1 ;
                O3_ESRL:llod_flag = -888888 ;
                O3_ESRL:standard_name = "O3_ESRL" ;
                O3_ESRL:ulod_flag = -777777 ;
                O3_ESRL:missing_value = -999999 ;
                O3_ESRL:ulod_value = "N/A" ;
        double UTC(POINTS);
                UTC:units = "s" ;
                UTC:fill_value = -999999.0 ;
                UTC:llod_value = "N/A" ;
                UTC:scale = 1 ;
                UTC:llod_flag = -888888 ;
                UTC:standard_name = "UTC" ;
                UTC:ulod_flag = -777777 ;
                UTC:missing_value = -999999 ;
                UTC:ulod_value = "N/A" ;


// global properties:
                :fmt = "1001" ;
                :n_header_lines = 409 ;
                :PI_NAME = "Shook, Michael" ;
                :ORGANIZATION_NAME = "NASA Atmospheric Composition Branch, NASA Langley Research Center (SSAI)" ;
                :SOURCE_DESCRIPTION = "Merged data file for DC3, Flights 01-18 (20120518-20120622), on the DC-8 platform. Data is merged to 60 seconds/timeline." ;
                :MISSION_NAME = "NSF DC3 Mission 2012" ;
                :VOLUME_INFO = "1, 1" ;
                :SDATE = "20120518" ;
                :WDATE = "20160113" ;
                :TIME_INTERVAL = "-1" ;
                :INDEPENDENT_VARIABLE = "Fractional_Day, none" ;
                :PI_CONTACT_INFO = "michael.shook@nasa.gov,jennifer.r.olson@nasa.gov,gao.chen@nasa.gov" ;
                :PLATFORM = "NASA Dryden DC-8 Aircraft" ;
                :LOCATION = "Latitude, Longitude, and Altitude included in data records" ;
                :ASSOCIATED_DATA = "N/A" ;
                :INSTRUMENT_INFO = "N/A" ;
                :DATA_INFO = "Please see PI data file for explanation of ULOD and LLOD." ;
                :UNCERTAINTY = "See individual files for uncertainty information." ;
                :ULOD_FLAG = "-777777" ;
                :ULOD_VALUE = "N/A" ;
                :LLOD_FLAG = "-888888" ;
                :LLOD_VALUE = "N/A" ;
                :DM_CONTACT_INFO = "gao.chen@nasa.gov" ;
                :PROJECT_INFO = "N/A" ;
                :STIPULATIONS_ON_USE = "N/A" ;
                :OTHER_COMMENTS = "This merge was created using data in the NASA DC3 archive" ;
                :as of 01/12/2016. = "as of 01/12/2016." ;
                :In most cases, variable names have been kept identical = "In most cases, variable names have been kept identical" ;
                :to those submitted in the raw data files. = "to those submitted in the raw data files." ;
                :However, in some cases, names have been changed = "However, in some cases, names have been changed" ;
                :(e.g., to eliminate duplication) = "(e.g., to eliminate duplication)" ;
                :Units have been standardized throughout the merge. = "Units have been standardized throughout the merge." ;
                :Contact michael.shook@nasa.gov with any questions as to which data was included. = "Contact michael.shook@nasa.gov with any questions as to which data was included." ;
                :REVISION = "R7" ;
                :R7 = "Includes data submitted as of 01/12/2016. See the readme file for a more detailed changelog." ;
                :R6 = "Includes data submitted as of 05/19/2015." ;
                :R5 = "Includes data submitted as of 06/09/2014." ;
                :R4 = "Includes data submitted as of 03/03/2014." ;
                :R3 = "Includes data submitted as of 11/26/2013." ;
                :R2 = "Includes data submitted as of 11/25/2013." ;
                :R1 = "Includes data submitted as of 03/26/2013." ;
                :R0 = "Includes data submitted as of 02/05/2013." ;
                :TFLAG = "Fractional_Day" ;
                :history = "/Users/barronh/Development/pseudonetcdf/scripts/pncdump.py --header -v Fractional_Day,UTC,O3_ESRL -f ffi1001 icartt/dc3-mrg60-dc8_merge_20120518_R7_thru20120622.ict;/Users/barronh/Development/pseudonetcdf/scripts/pncdump.py --header -v Fractional_Day,UTC,O3_ESRL -f ffi1001 icartt/dc3-mrg60-dc8_merge_20120518_R7_thru20120622.ict;" ;
}

In [ ]:

    




    

In [7]:

    

close()
plot([0,10], [0,10], linestyle = '-', color = 'g', label = '1:1')
plot([0,5], [0,10], linestyle = '-', color = 'r', label = '2:1')
plot([0,10], [0,5], linestyle = '-', color = 'b', label = '1:2')
legend()
#savefig('temp.png')


    

    
Out[7]:





<matplotlib.legend.Legend at 0x10f14cc88>






    

In [ ]:

    




    

In [8]:

    

from PseudoNetCDF import PNC
args = PNC('--format=ffi1001', \
           'icartt/dc3-mrg60-dc8_merge_20120518_R7_thru20120622.ict')
infile = args.ifiles[0]
fdays = infile.variables['Fractional_Day']
o3 = infile.variables['O3_ESRL']
close()
plot(fdays, o3)
xlabel('Fractional Day')
ylabel('Ozone ' + o3.units)
?tick_params


    

In [9]:

    

import datetime
from PseudoNetCDF import PNC
args = PNC('--format=ffi1001', 'icartt/dc3-mrg60-dc8_merge_20120518_R7_thru20120622.ict')
infile = args.ifiles[0]
fdays = infile.variables['Fractional_Day']
o3 = infile.variables['O3_ESRL']
offset = datetime.datetime(2011, 12, 31).timestamp()
xdate = [datetime.datetime.utcfromtimestamp(offset + fday * 24*3600) \
         for fday in fdays]
plot(xdate, o3);


    

In [10]:

    

import datetime
from PseudoNetCDF import PNC
args = PNC('--format=ffi1001', 'icartt/dc3-mrg60-dc8_merge_20120518_R7_thru20120622.ict')
infile = args.ifiles[0]
fdays = infile.variables['Fractional_Day']
o3 = infile.variables['O3_ESRL']
offset = datetime.datetime(2011, 12, 31).timestamp()
xdate = [datetime.datetime.utcfromtimestamp(offset + fday * 24*3600) \
         for fday in fdays]
figure(figsize = (16, 4))
tick_params(axis = 'both', labelsize = 20, )
plot(xdate, o3)
ax = plt.gca()
ax.xaxis.set_major_formatter(plt.matplotlib.dates.DateFormatter('%m/%d'))
ax.xaxis.set_major_locator(plt.matplotlib.dates.DayLocator(\
                                    bymonthday = [1, 5, 10, 15, 20, 25]))
plt.setp(ax.get_xticklabels(), rotation = 45);


    

In [11]:

    

!pncts.py \
    --matplotlibrc="figure.figsize=16,6"\
    --format=ffi1001 -v O3_ESRL --coordkeys Fractional_Day \
    --expr "time=Fractional_Day" \
    --expr "time.units='days since 2011-12-31'"\
    icartt/dc3-mrg60-dc8_merge_20120518_R7_thru20120622.ict dc3ts


    

    




**PNC://anaconda/lib/python3.5/site-packages/matplotlib/axes/_axes.py:519:UserWarning:
  No labelled objects found. Use label='...' kwarg on individual plots.
dc3tsO3_ESRL.png

In [12]:

    

%ls dc3ts*


    

    




dc3tsO3_ESRL.png

In [13]:

    

from PseudoNetCDF import PNC
args = PNC("--format=bpch,vertgrid='GEOS-5-NATIVE',nogroup=('IJ-AVG-$',)",
           "bpch/ctm.bpch.v10-01-public-Run0.2013050100")
infile = args.ifiles[0]
latb = infile.variables['latitude_bounds']
lonb = infile.variables['longitude_bounds']
ozone = infile.variables['O3'][:, 0].mean(0)


    

In [14]:

    

lone = np.append(lonb[0,0], lonb[:, 1])
late = np.append(latb[0,0], latb[:, 1])
LON, LAT = np.meshgrid(lone, late)


    

In [15]:

    

close()
pcolor(LON, LAT, ozone, vmin = 20, vmax = 65)
colorbar();


    

In [16]:

    

from PseudoNetCDF.coordutil import getmap
m = getmap(infile, resolution = 'c')


    

In [17]:

    

rcParams['font.size'] = 18
close()
m.pcolor(LON, LAT, ozone, vmin = 20, vmax = 65)
m.drawcoastlines()
m.drawcountries()
m.drawstates() # What options does this take?
cb = plt.colorbar(orientation = 'horizontal', label = 'O$_3$ ppb')


    

In [18]:

    

!pncmap.py -v O3 -f "bpch,nogroup=('IJ-AVG-$',)" \
-s layer72,0 -r time,mean --norm="Normalize(vmin=0,vmax=80)" \
bpch/ctm.bpch.v10-01-public-Run0.2013050100 srfmap
%ls srfmap*


    

    




**PNC:/Users/barronh/Development/pseudonetcdf/src/PseudoNetCDF/geoschemfiles/_bpch.py:866:UserWarning:
  vertgrid selected (GEOS-5-REDUCED) and output layers are not consistent; update to GEOS-5-NATIVE (e.g., bpch(..., vertgrid='GEOS-5-NATIVE') -f "bpch,vertgrid='GEOS-5-NATIVE'"
srfmapO3.png

In [19]:

    

!pncdump.py -v etam_pressure --full-indices c -f bpch bpch/ctm.bpch.v10-01-public-Run0.2013050100


    

    




**PNC:/Users/barronh/Development/pseudonetcdf/src/PseudoNetCDF/geoschemfiles/_bpch.py:866:UserWarning:
  vertgrid selected (GEOS-5-REDUCED) and output layers are not consistent; update to GEOS-5-NATIVE (e.g., bpch(..., vertgrid='GEOS-5-NATIVE') -f "bpch,vertgrid='GEOS-5-NATIVE'"
PseudoNetCDF.core._files.PseudoNetCDFFile bpch/ctm.bpch.v10-01-public-Run0.2013050100 {
dimensions:
        layer = 47 ;
        layer_bounds = 48 ;
        longitude = 72 ;
        latitude = 46 ;
        time = UNLIMITED // (1 currently) 
        nv = 2 ;
        tnv = 2 ;

variables:
        double etam_pressure(layer);
                etam_pressure:units = "hPa" ;
                etam_pressure:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ;
                etam_pressure:base_units = "hPa" ;
                etam_pressure:var_desc = "etam_pressure" ;
                etam_pressure:long_name = "etam_pressure" ;
        float layer_bounds(layer_bounds);
                layer_bounds:units = "level" ;
                layer_bounds:standard_name = "hybrid_sigma_pressure" ;
                layer_bounds:positive = "up" ;
                layer_bounds:long_name = "hybrid level at layer midpoints" ;
        double longitude(longitude);
                longitude:units = "degrees_east" ;
                longitude:axis = "X" ;
                longitude:standard_name = "longitude" ;
                longitude:base_units = "degrees_east" ;
                longitude:bounds = "longitude_bounds" ;
                longitude:long_name = "longitude" ;
        double etai_pressure(layer_bounds);
                etai_pressure:units = "hPa" ;
                etai_pressure:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ;
                etai_pressure:base_units = "hPa" ;
                etai_pressure:var_desc = "etai_pressure" ;
                etai_pressure:long_name = "etai_pressure" ;
        float layer(layer);
                layer:units = "level" ;
                layer:standard_name = "hybrid_sigma_pressure" ;
                layer:positive = "up" ;
                layer:long_name = "hybrid level at layer midpoints" ;
        double latitude(latitude);
                latitude:units = "degrees_north" ;
                latitude:axis = "Y" ;
                latitude:standard_name = "latitude" ;
                latitude:base_units = "degrees_north" ;
                latitude:bounds = "latitude_bounds" ;
                latitude:long_name = "latitude" ;
        double time(time);
                time:units = "hours since 1985-01-01 00:00:00 UTC" ;
                time:standard_name = "time" ;
                time:base_units = "hours since 1985-01-01 00:00:00 UTC" ;
                time:bounds = "time_bounds" ;
                time:var_desc = "time" ;
                time:long_name = "time" ;
        double longitude_bounds(longitude, nv);
                longitude_bounds:units = "degrees_east" ;
                longitude_bounds:axis = "X" ;
                longitude_bounds:standard_name = "longitude" ;
                longitude_bounds:base_units = "degrees_east" ;
                longitude_bounds:long_name = "longitude" ;
        double latitude_bounds(latitude, nv);
                latitude_bounds:units = "degrees_north" ;
                latitude_bounds:axis = "Y" ;
                latitude_bounds:standard_name = "latitude" ;
                latitude_bounds:base_units = "degrees_north" ;
                latitude_bounds:long_name = "latitude" ;
        double time_bounds(time, tnv);
                time_bounds:units = "hours since 1985-01-01 00:00:00 UTC" ;
                time_bounds:standard_name = "time_bounds" ;
                time_bounds:base_units = "hours since 1985-01-01 00:00:00 UTC" ;
                time_bounds:var_desc = "time_bounds" ;
                time_bounds:long_name = "time_bounds" ;


// global properties:
                :noscale = False ;
                :nogroup = False ;
                :ftype = b"CTM bin 02                              " ;
                :toptitle = b"GEOS-CHEM binary punch file v. 2.0                                              " ;
                :modelname = b"GEOSFP              " ;
                :modelres = array([ 5.,  4.], dtype=float32) ;
                :halfpolar = 1 ;
                :center180 = 1 ;
                :start_tau0 = 248328.0 ;
                :start_tau1 = 249072.0 ;
                :vertgrid = "GEOS-5-REDUCED" ;
                :Ap = array([  0.00000000e+00,   4.80482600e-02,   6.59375200e+00,
         1.31348000e+01,   1.96131100e+01,   2.60920100e+01,
         3.25708100e+01,   3.89820100e+01,   4.53390100e+01,
         5.16961100e+01,   5.80532100e+01,   6.43626400e+01,
         7.06219800e+01,   7.88342200e+01,   8.90999200e+01,
         9.93652100e+01,   1.09181700e+02,   1.18958600e+02,
         1.28695900e+02,   1.42910000e+02,   1.56260000e+02,
         1.69609000e+02,   1.81619000e+02,   1.93097000e+02,
         2.03259000e+02,   2.12150000e+02,   2.18776000e+02,
         2.23898000e+02,   2.24363000e+02,   2.16865000e+02,
         2.01192000e+02,   1.76930000e+02,   1.50393000e+02,
         1.27837000e+02,   1.08663000e+02,   9.23657200e+01,
         7.85123100e+01,   5.63879100e+01,   4.01754100e+01,
         2.83678100e+01,   1.97916000e+01,   9.29294200e+00,
         4.07657100e+00,   1.65079000e+00,   6.16779100e-01,
         2.11349000e-01,   6.60000100e-02,   1.00000000e-02]) ;
                :Bp = array([  1.00000000e+00,   9.84952000e-01,   9.63406000e-01,
         9.41865000e-01,   9.20387000e-01,   8.98908000e-01,
         8.77429000e-01,   8.56018000e-01,   8.34660900e-01,
         8.13303900e-01,   7.91946900e-01,   7.70637500e-01,
         7.49378200e-01,   7.21166000e-01,   6.85899900e-01,
         6.50634900e-01,   6.15818400e-01,   5.81041500e-01,
         5.46304200e-01,   4.94590200e-01,   4.43740200e-01,
         3.92891100e-01,   3.43381100e-01,   2.94403100e-01,
         2.46741100e-01,   2.00350100e-01,   1.56224100e-01,
         1.13602100e-01,   6.37200600e-02,   2.80100400e-02,
         6.96002500e-03,   8.17541300e-09,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00,
         0.00000000e+00,   0.00000000e+00,   0.00000000e+00]) ;
                :Conventions = "CF-1.6" ;
                :history = "/Users/barronh/Development/pseudonetcdf/scripts/pncdump.py -v etam_pressure --full-indices c -f bpch bpch/ctm.bpch.v10-01-public-Run0.2013050100;/Users/barronh/Development/pseudonetcdf/scripts/pncdump.py -v etam_pressure --full-indices c -f bpch bpch/ctm.bpch.v10-01-public-Run0.2013050100;" ;


data:
 etam_pressure =
  1005.65033113, // etam_pressure(0,) 
  990.40777188, // etam_pressure(1,) 
  975.1221963749999, // etam_pressure(2,) 
  959.8373744999999, // etam_pressure(3,) 
  944.5528893749999, // etam_pressure(4,) 
  929.268142625, // etam_pressure(5,) 
  913.9839963750001, // etam_pressure(6,) 
  898.7007077125, // etam_pressure(7,) 
  883.4177268, // etam_pressure(8,) 
  868.1348465499999, // etam_pressure(9,) 
  852.85224665, // etam_pressure(10,) 
  837.5702640125, // etam_pressure(11,) 
  819.742555325, // etam_pressure(12,) 
  796.8218315875001, // etam_pressure(13,) 
  771.3545080499999, // etam_pressure(14,) 
  745.8903581125001, // etam_pressure(15,) 
  720.4292968375, // etam_pressure(16,) 
  694.9687652625, // etam_pressure(17,) 
  663.1460754, // etam_pressure(18,) 
  624.9666388999999, // etam_pressure(19,) 
  586.7928323625, // etam_pressure(20,) 
  548.6279033249999, // etam_pressure(21,) 
  510.475420325, // etam_pressure(22,) 
  472.335180325, // etam_pressure(23,) 
  434.2120792, // etam_pressure(24,) 
  396.112404075, // etam_pressure(25,) 
  358.037698575, // etam_pressure(26,) 
  313.96633931, // etam_pressure(27,) 
  267.0867619125, // etam_pressure(28,) 
  226.745209180625, // etam_pressure(29,) 
  192.5871268074936, // etam_pressure(30,) 
  163.6615041418686, // etam_pressure(31,) 
  139.115, // etam_pressure(32,) 
  118.25, // etam_pressure(33,) 
  100.51436, // etam_pressure(34,) 
  85.439015, // etam_pressure(35,) 
  67.45011, // etam_pressure(36,) 
  48.28166, // etam_pressure(37,) 
  34.27161, // etam_pressure(38,) 
  24.079705, // etam_pressure(39,) 
  14.542271, // etam_pressure(40,) 
  6.684756500000001, // etam_pressure(41,) 
  2.8636805, // etam_pressure(42,) 
  1.13378455, // etam_pressure(43,) 
  0.41406405, // etam_pressure(44,) 
  0.138674505, // etam_pressure(45,) 
  0.038000005; // etam_pressure(46,) 
 layer_bounds =
  0, // layer_bounds(0,) 
  1, // layer_bounds(1,) 
  2, // layer_bounds(2,) 
  3, // layer_bounds(3,) 
  4, // layer_bounds(4,) 
  5, // layer_bounds(5,) 
  6, // layer_bounds(6,) 
  7, // layer_bounds(7,) 
  8, // layer_bounds(8,) 
  9, // layer_bounds(9,) 
  10, // layer_bounds(10,) 
  11, // layer_bounds(11,) 
  12, // layer_bounds(12,) 
  13, // layer_bounds(13,) 
  14, // layer_bounds(14,) 
  15, // layer_bounds(15,) 
  16, // layer_bounds(16,) 
  17, // layer_bounds(17,) 
  18, // layer_bounds(18,) 
  19, // layer_bounds(19,) 
  20, // layer_bounds(20,) 
  21, // layer_bounds(21,) 
  22, // layer_bounds(22,) 
  23, // layer_bounds(23,) 
  24, // layer_bounds(24,) 
  25, // layer_bounds(25,) 
  26, // layer_bounds(26,) 
  27, // layer_bounds(27,) 
  28, // layer_bounds(28,) 
  29, // layer_bounds(29,) 
  30, // layer_bounds(30,) 
  31, // layer_bounds(31,) 
  32, // layer_bounds(32,) 
  33, // layer_bounds(33,) 
  34, // layer_bounds(34,) 
  35, // layer_bounds(35,) 
  36, // layer_bounds(36,) 
  37, // layer_bounds(37,) 
  38, // layer_bounds(38,) 
  39, // layer_bounds(39,) 
  40, // layer_bounds(40,) 
  41, // layer_bounds(41,) 
  42, // layer_bounds(42,) 
  43, // layer_bounds(43,) 
  44, // layer_bounds(44,) 
  45, // layer_bounds(45,) 
  46, // layer_bounds(46,) 
  47; // layer_bounds(47,) 
 longitude =
  -180, // longitude(0,) 
  -175, // longitude(1,) 
  -170, // longitude(2,) 
  -165, // longitude(3,) 
  -160, // longitude(4,) 
  -155, // longitude(5,) 
  -150, // longitude(6,) 
  -145, // longitude(7,) 
  -140, // longitude(8,) 
  -135, // longitude(9,) 
  -130, // longitude(10,) 
  -125, // longitude(11,) 
  -120, // longitude(12,) 
  -115, // longitude(13,) 
  -110, // longitude(14,) 
  -105, // longitude(15,) 
  -100, // longitude(16,) 
  -95, // longitude(17,) 
  -90, // longitude(18,) 
  -85, // longitude(19,) 
  -80, // longitude(20,) 
  -75, // longitude(21,) 
  -70, // longitude(22,) 
  -65, // longitude(23,) 
  -60, // longitude(24,) 
  -55, // longitude(25,) 
  -50, // longitude(26,) 
  -45, // longitude(27,) 
  -40, // longitude(28,) 
  -35, // longitude(29,) 
  -30, // longitude(30,) 
  -25, // longitude(31,) 
  -20, // longitude(32,) 
  -15, // longitude(33,) 
  -10, // longitude(34,) 
  -5, // longitude(35,) 
  0, // longitude(36,) 
  5, // longitude(37,) 
  10, // longitude(38,) 
  15, // longitude(39,) 
  20, // longitude(40,) 
  25, // longitude(41,) 
  30, // longitude(42,) 
  35, // longitude(43,) 
  40, // longitude(44,) 
  45, // longitude(45,) 
  50, // longitude(46,) 
  55, // longitude(47,) 
  60, // longitude(48,) 
  65, // longitude(49,) 
  70, // longitude(50,) 
  75, // longitude(51,) 
  80, // longitude(52,) 
  85, // longitude(53,) 
  90, // longitude(54,) 
  95, // longitude(55,) 
  100, // longitude(56,) 
  105, // longitude(57,) 
  110, // longitude(58,) 
  115, // longitude(59,) 
  120, // longitude(60,) 
  125, // longitude(61,) 
  130, // longitude(62,) 
  135, // longitude(63,) 
  140, // longitude(64,) 
  145, // longitude(65,) 
  150, // longitude(66,) 
  155, // longitude(67,) 
  160, // longitude(68,) 
  165, // longitude(69,) 
  170, // longitude(70,) 
  175; // longitude(71,) 
 etai_pressure =
  1013.25, // etai_pressure(0,) 
  998.05066226, // etai_pressure(1,) 
  982.7648815, // etai_pressure(2,) 
  967.47951125, // etai_pressure(3,) 
  952.1952377499999, // etai_pressure(4,) 
  936.910541, // etai_pressure(5,) 
  921.62574425, // etai_pressure(6,) 
  906.3422484999999, // etai_pressure(7,) 
  891.0591669250001, // etai_pressure(8,) 
  875.7762866749999, // etai_pressure(9,) 
  860.493406425, // etai_pressure(10,) 
  845.2110868749999, // etai_pressure(11,) 
  829.92944115, // etai_pressure(12,) 
  809.5556694999999, // etai_pressure(13,) 
  784.087993675, // etai_pressure(14,) 
  758.6210224250001, // etai_pressure(15,) 
  733.1596938, // etai_pressure(16,) 
  707.6988998750001, // etai_pressure(17,) 
  682.23863065, // etai_pressure(18,) 
  644.0535201499999, // etai_pressure(19,) 
  605.87975765, // etai_pressure(20,) 
  567.705907075, // etai_pressure(21,) 
  529.549899575, // etai_pressure(22,) 
  491.400941075, // etai_pressure(23,) 
  453.269419575, // etai_pressure(24,) 
  415.154738825, // etai_pressure(25,) 
  377.070069325, // etai_pressure(26,) 
  339.005327825, // etai_pressure(27,) 
  288.927350795, // etai_pressure(28,) 
  245.24617303, // etai_pressure(29,) 
  208.24424533125, // etai_pressure(30,) 
  176.9300082837372, // etai_pressure(31,) 
  150.393, // etai_pressure(32,) 
  127.837, // etai_pressure(33,) 
  108.663, // etai_pressure(34,) 
  92.36572, // etai_pressure(35,) 
  78.51231, // etai_pressure(36,) 
  56.38791, // etai_pressure(37,) 
  40.17541, // etai_pressure(38,) 
  28.36781, // etai_pressure(39,) 
  19.7916, // etai_pressure(40,) 
  9.292942, // etai_pressure(41,) 
  4.076571, // etai_pressure(42,) 
  1.65079, // etai_pressure(43,) 
  0.6167791, // etai_pressure(44,) 
  0.211349, // etai_pressure(45,) 
  0.06600001, // etai_pressure(46,) 
  0.01; // etai_pressure(47,) 
 layer =
  1, // layer(0,) 
  2, // layer(1,) 
  3, // layer(2,) 
  4, // layer(3,) 
  5, // layer(4,) 
  6, // layer(5,) 
  7, // layer(6,) 
  8, // layer(7,) 
  9, // layer(8,) 
  10, // layer(9,) 
  11, // layer(10,) 
  12, // layer(11,) 
  13, // layer(12,) 
  14, // layer(13,) 
  15, // layer(14,) 
  16, // layer(15,) 
  17, // layer(16,) 
  18, // layer(17,) 
  19, // layer(18,) 
  20, // layer(19,) 
  21, // layer(20,) 
  22, // layer(21,) 
  23, // layer(22,) 
  24, // layer(23,) 
  25, // layer(24,) 
  26, // layer(25,) 
  27, // layer(26,) 
  28, // layer(27,) 
  29, // layer(28,) 
  30, // layer(29,) 
  31, // layer(30,) 
  32, // layer(31,) 
  33, // layer(32,) 
  34, // layer(33,) 
  35, // layer(34,) 
  36, // layer(35,) 
  37, // layer(36,) 
  38, // layer(37,) 
  39, // layer(38,) 
  40, // layer(39,) 
  41, // layer(40,) 
  42, // layer(41,) 
  43, // layer(42,) 
  44, // layer(43,) 
  45, // layer(44,) 
  46, // layer(45,) 
  47; // layer(46,) 
 latitude =
  -89, // latitude(0,) 
  -86, // latitude(1,) 
  -82, // latitude(2,) 
  -78, // latitude(3,) 
  -74, // latitude(4,) 
  -70, // latitude(5,) 
  -66, // latitude(6,) 
  -62, // latitude(7,) 
  -58, // latitude(8,) 
  -54, // latitude(9,) 
  -50, // latitude(10,) 
  -46, // latitude(11,) 
  -42, // latitude(12,) 
  -38, // latitude(13,) 
  -34, // latitude(14,) 
  -30, // latitude(15,) 
  -26, // latitude(16,) 
  -22, // latitude(17,) 
  -18, // latitude(18,) 
  -14, // latitude(19,) 
  -10, // latitude(20,) 
  -6, // latitude(21,) 
  -2, // latitude(22,) 
  2, // latitude(23,) 
  6, // latitude(24,) 
  10, // latitude(25,) 
  14, // latitude(26,) 
  18, // latitude(27,) 
  22, // latitude(28,) 
  26, // latitude(29,) 
  30, // latitude(30,) 
  34, // latitude(31,) 
  38, // latitude(32,) 
  42, // latitude(33,) 
  46, // latitude(34,) 
  50, // latitude(35,) 
  54, // latitude(36,) 
  58, // latitude(37,) 
  62, // latitude(38,) 
  66, // latitude(39,) 
  70, // latitude(40,) 
  74, // latitude(41,) 
  78, // latitude(42,) 
  82, // latitude(43,) 
  86, // latitude(44,) 
  89; // latitude(45,) 
 time =
  248700; // time(0,) 
 longitude_bounds =
  -182.5, // longitude_bounds(0, 0) 
  -177.5, // longitude_bounds(0, 1) 
  -177.5, // longitude_bounds(1, 0) 
  -172.5, // longitude_bounds(1, 1) 
  -172.5, // longitude_bounds(2, 0) 
  -167.5, // longitude_bounds(2, 1) 
  -167.5, // longitude_bounds(3, 0) 
  -162.5, // longitude_bounds(3, 1) 
  -162.5, // longitude_bounds(4, 0) 
  -157.5, // longitude_bounds(4, 1) 
  -157.5, // longitude_bounds(5, 0) 
  -152.5, // longitude_bounds(5, 1) 
  -152.5, // longitude_bounds(6, 0) 
  -147.5, // longitude_bounds(6, 1) 
  -147.5, // longitude_bounds(7, 0) 
  -142.5, // longitude_bounds(7, 1) 
  -142.5, // longitude_bounds(8, 0) 
  -137.5, // longitude_bounds(8, 1) 
  -137.5, // longitude_bounds(9, 0) 
  -132.5, // longitude_bounds(9, 1) 
  -132.5, // longitude_bounds(10, 0) 
  -127.5, // longitude_bounds(10, 1) 
  -127.5, // longitude_bounds(11, 0) 
  -122.5, // longitude_bounds(11, 1) 
  -122.5, // longitude_bounds(12, 0) 
  -117.5, // longitude_bounds(12, 1) 
  -117.5, // longitude_bounds(13, 0) 
  -112.5, // longitude_bounds(13, 1) 
  -112.5, // longitude_bounds(14, 0) 
  -107.5, // longitude_bounds(14, 1) 
  -107.5, // longitude_bounds(15, 0) 
  -102.5, // longitude_bounds(15, 1) 
  -102.5, // longitude_bounds(16, 0) 
  -97.5, // longitude_bounds(16, 1) 
  -97.5, // longitude_bounds(17, 0) 
  -92.5, // longitude_bounds(17, 1) 
  -92.5, // longitude_bounds(18, 0) 
  -87.5, // longitude_bounds(18, 1) 
  -87.5, // longitude_bounds(19, 0) 
  -82.5, // longitude_bounds(19, 1) 
  -82.5, // longitude_bounds(20, 0) 
  -77.5, // longitude_bounds(20, 1) 
  -77.5, // longitude_bounds(21, 0) 
  -72.5, // longitude_bounds(21, 1) 
  -72.5, // longitude_bounds(22, 0) 
  -67.5, // longitude_bounds(22, 1) 
  -67.5, // longitude_bounds(23, 0) 
  -62.5, // longitude_bounds(23, 1) 
  -62.5, // longitude_bounds(24, 0) 
  -57.5, // longitude_bounds(24, 1) 
  -57.5, // longitude_bounds(25, 0) 
  -52.5, // longitude_bounds(25, 1) 
  -52.5, // longitude_bounds(26, 0) 
  -47.5, // longitude_bounds(26, 1) 
  -47.5, // longitude_bounds(27, 0) 
  -42.5, // longitude_bounds(27, 1) 
  -42.5, // longitude_bounds(28, 0) 
  -37.5, // longitude_bounds(28, 1) 
  -37.5, // longitude_bounds(29, 0) 
  -32.5, // longitude_bounds(29, 1) 
  -32.5, // longitude_bounds(30, 0) 
  -27.5, // longitude_bounds(30, 1) 
  -27.5, // longitude_bounds(31, 0) 
  -22.5, // longitude_bounds(31, 1) 
  -22.5, // longitude_bounds(32, 0) 
  -17.5, // longitude_bounds(32, 1) 
  -17.5, // longitude_bounds(33, 0) 
  -12.5, // longitude_bounds(33, 1) 
  -12.5, // longitude_bounds(34, 0) 
  -7.5, // longitude_bounds(34, 1) 
  -7.5, // longitude_bounds(35, 0) 
  -2.5, // longitude_bounds(35, 1) 
  -2.5, // longitude_bounds(36, 0) 
  2.5, // longitude_bounds(36, 1) 
  2.5, // longitude_bounds(37, 0) 
  7.5, // longitude_bounds(37, 1) 
  7.5, // longitude_bounds(38, 0) 
  12.5, // longitude_bounds(38, 1) 
  12.5, // longitude_bounds(39, 0) 
  17.5, // longitude_bounds(39, 1) 
  17.5, // longitude_bounds(40, 0) 
  22.5, // longitude_bounds(40, 1) 
  22.5, // longitude_bounds(41, 0) 
  27.5, // longitude_bounds(41, 1) 
  27.5, // longitude_bounds(42, 0) 
  32.5, // longitude_bounds(42, 1) 
  32.5, // longitude_bounds(43, 0) 
  37.5, // longitude_bounds(43, 1) 
  37.5, // longitude_bounds(44, 0) 
  42.5, // longitude_bounds(44, 1) 
  42.5, // longitude_bounds(45, 0) 
  47.5, // longitude_bounds(45, 1) 
  47.5, // longitude_bounds(46, 0) 
  52.5, // longitude_bounds(46, 1) 
  52.5, // longitude_bounds(47, 0) 
  57.5, // longitude_bounds(47, 1) 
  57.5, // longitude_bounds(48, 0) 
  62.5, // longitude_bounds(48, 1) 
  62.5, // longitude_bounds(49, 0) 
  67.5, // longitude_bounds(49, 1) 
  67.5, // longitude_bounds(50, 0) 
  72.5, // longitude_bounds(50, 1) 
  72.5, // longitude_bounds(51, 0) 
  77.5, // longitude_bounds(51, 1) 
  77.5, // longitude_bounds(52, 0) 
  82.5, // longitude_bounds(52, 1) 
  82.5, // longitude_bounds(53, 0) 
  87.5, // longitude_bounds(53, 1) 
  87.5, // longitude_bounds(54, 0) 
  92.5, // longitude_bounds(54, 1) 
  92.5, // longitude_bounds(55, 0) 
  97.5, // longitude_bounds(55, 1) 
  97.5, // longitude_bounds(56, 0) 
  102.5, // longitude_bounds(56, 1) 
  102.5, // longitude_bounds(57, 0) 
  107.5, // longitude_bounds(57, 1) 
  107.5, // longitude_bounds(58, 0) 
  112.5, // longitude_bounds(58, 1) 
  112.5, // longitude_bounds(59, 0) 
  117.5, // longitude_bounds(59, 1) 
  117.5, // longitude_bounds(60, 0) 
  122.5, // longitude_bounds(60, 1) 
  122.5, // longitude_bounds(61, 0) 
  127.5, // longitude_bounds(61, 1) 
  127.5, // longitude_bounds(62, 0) 
  132.5, // longitude_bounds(62, 1) 
  132.5, // longitude_bounds(63, 0) 
  137.5, // longitude_bounds(63, 1) 
  137.5, // longitude_bounds(64, 0) 
  142.5, // longitude_bounds(64, 1) 
  142.5, // longitude_bounds(65, 0) 
  147.5, // longitude_bounds(65, 1) 
  147.5, // longitude_bounds(66, 0) 
  152.5, // longitude_bounds(66, 1) 
  152.5, // longitude_bounds(67, 0) 
  157.5, // longitude_bounds(67, 1) 
  157.5, // longitude_bounds(68, 0) 
  162.5, // longitude_bounds(68, 1) 
  162.5, // longitude_bounds(69, 0) 
  167.5, // longitude_bounds(69, 1) 
  167.5, // longitude_bounds(70, 0) 
  172.5, // longitude_bounds(70, 1) 
  172.5, // longitude_bounds(71, 0) 
  177.5; // longitude_bounds(71, 1) 
 latitude_bounds =
  -90, // latitude_bounds(0, 0) 
  -88, // latitude_bounds(0, 1) 
  -88, // latitude_bounds(1, 0) 
  -84, // latitude_bounds(1, 1) 
  -84, // latitude_bounds(2, 0) 
  -80, // latitude_bounds(2, 1) 
  -80, // latitude_bounds(3, 0) 
  -76, // latitude_bounds(3, 1) 
  -76, // latitude_bounds(4, 0) 
  -72, // latitude_bounds(4, 1) 
  -72, // latitude_bounds(5, 0) 
  -68, // latitude_bounds(5, 1) 
  -68, // latitude_bounds(6, 0) 
  -64, // latitude_bounds(6, 1) 
  -64, // latitude_bounds(7, 0) 
  -60, // latitude_bounds(7, 1) 
  -60, // latitude_bounds(8, 0) 
  -56, // latitude_bounds(8, 1) 
  -56, // latitude_bounds(9, 0) 
  -52, // latitude_bounds(9, 1) 
  -52, // latitude_bounds(10, 0) 
  -48, // latitude_bounds(10, 1) 
  -48, // latitude_bounds(11, 0) 
  -44, // latitude_bounds(11, 1) 
  -44, // latitude_bounds(12, 0) 
  -40, // latitude_bounds(12, 1) 
  -40, // latitude_bounds(13, 0) 
  -36, // latitude_bounds(13, 1) 
  -36, // latitude_bounds(14, 0) 
  -32, // latitude_bounds(14, 1) 
  -32, // latitude_bounds(15, 0) 
  -28, // latitude_bounds(15, 1) 
  -28, // latitude_bounds(16, 0) 
  -24, // latitude_bounds(16, 1) 
  -24, // latitude_bounds(17, 0) 
  -20, // latitude_bounds(17, 1) 
  -20, // latitude_bounds(18, 0) 
  -16, // latitude_bounds(18, 1) 
  -16, // latitude_bounds(19, 0) 
  -12, // latitude_bounds(19, 1) 
  -12, // latitude_bounds(20, 0) 
  -8, // latitude_bounds(20, 1) 
  -8, // latitude_bounds(21, 0) 
  -4, // latitude_bounds(21, 1) 
  -4, // latitude_bounds(22, 0) 
  0, // latitude_bounds(22, 1) 
  0, // latitude_bounds(23, 0) 
  4, // latitude_bounds(23, 1) 
  4, // latitude_bounds(24, 0) 
  8, // latitude_bounds(24, 1) 
  8, // latitude_bounds(25, 0) 
  12, // latitude_bounds(25, 1) 
  12, // latitude_bounds(26, 0) 
  16, // latitude_bounds(26, 1) 
  16, // latitude_bounds(27, 0) 
  20, // latitude_bounds(27, 1) 
  20, // latitude_bounds(28, 0) 
  24, // latitude_bounds(28, 1) 
  24, // latitude_bounds(29, 0) 
  28, // latitude_bounds(29, 1) 
  28, // latitude_bounds(30, 0) 
  32, // latitude_bounds(30, 1) 
  32, // latitude_bounds(31, 0) 
  36, // latitude_bounds(31, 1) 
  36, // latitude_bounds(32, 0) 
  40, // latitude_bounds(32, 1) 
  40, // latitude_bounds(33, 0) 
  44, // latitude_bounds(33, 1) 
  44, // latitude_bounds(34, 0) 
  48, // latitude_bounds(34, 1) 
  48, // latitude_bounds(35, 0) 
  52, // latitude_bounds(35, 1) 
  52, // latitude_bounds(36, 0) 
  56, // latitude_bounds(36, 1) 
  56, // latitude_bounds(37, 0) 
  60, // latitude_bounds(37, 1) 
  60, // latitude_bounds(38, 0) 
  64, // latitude_bounds(38, 1) 
  64, // latitude_bounds(39, 0) 
  68, // latitude_bounds(39, 1) 
  68, // latitude_bounds(40, 0) 
  72, // latitude_bounds(40, 1) 
  72, // latitude_bounds(41, 0) 
  76, // latitude_bounds(41, 1) 
  76, // latitude_bounds(42, 0) 
  80, // latitude_bounds(42, 1) 
  80, // latitude_bounds(43, 0) 
  84, // latitude_bounds(43, 1) 
  84, // latitude_bounds(44, 0) 
  88, // latitude_bounds(44, 1) 
  88, // latitude_bounds(45, 0) 
  90; // latitude_bounds(45, 1) 
 time_bounds =
  248328, // time_bounds(0, 0) 
  249072; // time_bounds(0, 1) 
}

In [26]:

    

!pncmap.py -f "bpch,nogroup=('IJ-AVG-\$',)" -v O3 -s layer72,? \
    bpch/ctm.bpch.v10-01-public-Run0.2013050100 map500hPa_


    

    




**PNC:/Users/barronh/Development/pseudonetcdf/src/PseudoNetCDF/geoschemfiles/_bpch.py:866:UserWarning:
  vertgrid selected (GEOS-5-REDUCED) and output layers are not consistent; update to GEOS-5-NATIVE (e.g., bpch(..., vertgrid='GEOS-5-NATIVE') -f "bpch,vertgrid='GEOS-5-NATIVE'"
**PNC:/Users/barronh/Development/pseudonetcdf/src/PseudoNetCDF/plotutil/pncmap.py:85:UserWarning:
  Autoselect deciles colormap of O3; override width --norm

In [27]:

    

!pncgen.py -O -f ffi1001 \
            --mask "where,PRESSURE>515.7865" \
            --mask "where,PRESSURE<479.60059" \
            --rename v,O3_ESRL,O3 --rename v,LATITUDE,latitude \
            -v Fractional_Day,O3_ESRL,LATITUDE,LONGITUDE,PRESSURE \
            --expr "longitude=np.where(LONGITUDE>180,LONGITUDE-360,LONGITUDE)" \
            --expr "time=Fractional_Day*24*3600" \
            --expr "time.units='seconds since 2011-12-31'" \
            icartt/dc3-mrg60-dc8_merge_20120518_R7_thru20120622.ict dc3.nc


    

    




**PNC:/Users/barronh/Development/pseudonetcdf/src/PseudoNetCDF/pncgen.py:78:UserWarning:
  Could not add as of 01/12/2016. to file; <class 'AttributeError'>: NetCDF: Name contains illegal characters
**PNC:/Users/barronh/Development/pseudonetcdf/src/PseudoNetCDF/pncgen.py:78:UserWarning:
  Could not add (e.g., to eliminate duplication) to file; <class 'AttributeError'>: NetCDF: Name contains illegal characters

In [28]:

    

!pncgen.py -O -f "bpch,nogroup=('IJ-AVG-$',),vertgrid='GEOS-5-NATIVE'" \
         --stack=time -s latitude,28,36 -s longitude,10,25 \
         -s layer72,22 -r time,mean -v O3 \
         bpch/ctm.bpch.v10-01-public-Run0.2013050100 bpch/ctm.bpch.v10-01-public-Run0.2013060100 \
         bpch_500hPa.nc


    

    




**PNC:/Users/barronh/Development/pseudonetcdf/src/PseudoNetCDF/core/_functions.py:831:UserWarning:
  Got duplicate variables for layer72 without stackable dimension; first value retained

In [29]:

    

!pncmap.py --overlay --norm="Normalize(0, 100)" -v O3 \
 bpch_500hPa.nc dc3.nc dc3bpchmap
%ls dc3bpchmap*


    

    




**PNC:/Users/barronh/Development/pseudonetcdf/src/PseudoNetCDF/coordutil.py:181:UserWarning:
  Latitude bounds are approximate
dc3bpchmapO30.png  dc3bpchmapO31.png

In [33]:

    

!pncscatter.py -v O3 \
        --plot-commands="plt.xlabel('Obs')" \
        --plot-commands="plt.ylabel('Mod')" \
        dc3.nc bpch_500hPa.nc scat
!pnceval.py --funcs=MB,ME -v O3 dc3.nc bpch_500hPa.nc


    

    




dc3nc_0 = ifile0 = dc3.nc
bpch_5_0 = ifile1 = bpch_500hPa.nc
**PNC:/Users/barronh/Development/pseudonetcdf/src/PseudoNetCDF/pnceval.py:371:UserWarning:
  Assumes input order is obs model
**PNC:/Users/barronh/Development/pseudonetcdf/src/PseudoNetCDF/pnceval.py:378:UserWarning:
  Skipped MB;operands could not be broadcast together with shapes (1,1,8,15) (6817,) 
**PNC:/Users/barronh/Development/pseudonetcdf/src/PseudoNetCDF/pnceval.py:378:UserWarning:
  Skipped ME;operands could not be broadcast together with shapes (1,1,8,15) (6817,) 

In [25]:

    

!pnceval.py --help


    

    




usage: pnceval.py [-h] [--verbose] [--pnc PNC]
                  [-f {see --list-formats for choices}]
                  [--list-format] [--help-format HELPFORMAT]
                  [--sep] [--inherit] [--mangle]
                  [--rename RENAME]
                  [--remove-singleton REMOVESINGLETON]
                  [--coordkeys key1,key2]
                  [-v varname1[,varname2[,...,varnameN]]
                  [-a att_nm,var_nm,mode,att_typ,att_val]
                  [-m MASKS] [--from-convention FROMCONV]
                  [--to-convention TOCONV] [--stack STACK]
                  [--merge] [-s dim,start[,stop[,step]]]
                  [-r dim,function[,weight]]
                  [--mesh dim,weight,function]
                  [-c dim,mode,wgt1,wgt2,...wgtN] [-e EXTRACT]
                  [--extract-file EXTRACTFILE]
                  [--extractmethod {nn,linear,cubic,quintic,KDTree}]
                  [--op-typ OPERATORS] [--expr EXPRESSIONS]
                  [--exprscript EXPRESSIONSCRIPTS] [-i] [-H]
                  [-t] [--full-indices [c|f]] [-l LEN]
                  [--float-precision FDIG]
                  [--double-precision PDIG]
                  [--dump-name CDLNAME] [--funcs FUNCS]
                  [ifiles [ifiles ...]]

PseudoNetCDF Argument Parsing

positional arguments:
  ifiles                path to a file formatted as type -f

optional arguments:
  -h, --help            show this help message and exit
  --verbose             Provides verbosity with pncgen
  --pnc PNC             Set of pseudonetcdf commands to be
                        process separately
  -f {see --list-formats for choices}, --format {see --list-formats for choices}
                        File format (default netcdf), can be
                        one of the choices listed, or an
                        expression that evaluates to a reader.
                        Keyword arguments are passed via
                        ,kwd=value.
  --list-format         Show format options for -f
  --help-format HELPFORMAT
                        Show help for file format (must be one
                        of the options for -f)
  --sep                 Used to separate groups of arguments
                        for parsing (e.g., pncgen -- [options1]
                        file(s)1 [--sep [options2] file(s)2
                        [... [--sep [optionsN] file(s)N]]
  --inherit             Allow subparsed sections (separated
                        with -- and --sep) to inherit from
                        global options (-f, --format is always
                        inherited).
  --mangle              Remove non-standard ascii from names
  --rename RENAME       Provide pairs of strings to be
                        substituted --rename=type,oldkey,newkey
                        (type: v = variable; d = dimension;)
  --remove-singleton REMOVESINGLETON
                        Remove singleton (length 1) dimensions
  --coordkeys key1,key2
                        Variables to be ignored in pncbo.
  -v varname1[,varname2[,...,varnameN], --variables varname1[,varname2[,...,varnameN]
                        Variable names or regular expressions
                        (using match) separated by ','. If a
                        group(s) has been specified, only
                        variables in that (those) group(s) will
                        be selected.
  -a att_nm,var_nm,mode,att_typ,att_val, --attribute att_nm,var_nm,mode,att_typ,att_val
                        Variables have attributes that can be
                        added following nco syntax (--attribute
                        att_nm,var_nm,mode,att_typ,att_val);
                        mode = a,c,d,m,o and att_typ =
                        f,d,l,s,c,b; att_typ is any valid numpy
                        type.
  -m MASKS, --mask MASKS
                        Masks to apply (e.g., greater,0 or
                        less,0 or values,0, or where,(time[:]%2
                        4<12)[:,None].repeat(10,1))
  --from-convention FROMCONV
                        From convention currently only support
                        ioapi
  --to-convention TOCONV
                        To convention currently only supports
                        cf
  --stack STACK         Concatentate (stack) files on the
                        dimension.
  --merge               Combine variables into one file
  -s dim,start[,stop[,step]], --slice dim,start[,stop[,step]]
                        Variables have dimensions (time, layer,
                        lat, lon), which can be subset using
                        dim,start,stop,stride (e.g.,
                        --slice=layer,0,47,5 would sample every
                        fifth layer starting at 0)
  -r dim,function[,weight], --reduce dim,function[,weight]
                        Variable dimensions can be reduced
                        using dim,function,weight syntax (e.g.,
                        --reduce=layer,mean,weight). Weighting
                        is not fully functional.
  --mesh dim,weight,function
                        Variable dimensions can be meshed using
                        dim,function,weight syntax (e.g.,
                        --mesh=time,0.5,mean).
  -c dim,mode,wgt1,wgt2,...wgtN, --convolve dim,mode,wgt1,wgt2,...wgtN
                        Variable dimension is reduced by
                        convolve function
                        (dim,mode,wgt1,wgt2,...wgtN)
  -e EXTRACT, --extract EXTRACT
                        lon/lat coordinates to extract lon1,lat
                        1/lon2,lat2/lon3,lat3/.../lonN,latN
  --extract-file EXTRACTFILE
                        pncparse options for file
  --extractmethod {nn,linear,cubic,quintic,KDTree}
                        Method for extraction
  --op-typ OPERATORS    Operator for binary file operations.
                        Binary file operations use the first
                        two files, then the result and the next
                        file, etc. Use // or <= or % or is not
                        or >> or & or == or != or + or * or -
                        or / or < or >= or ** or > or << or |
                        or is or ^
  --expr EXPRESSIONS    Generic expressions to execute in the
                        context of the file.
  --exprscript EXPRESSIONSCRIPTS
                        Generic expressions to execute in the
                        context of the file.
  -i, --interactive     Use interactive mode
  -H, --header
  -t, --timestring
  --full-indices [c|f]  Provide indices in CDL using either C
                        or Fortran style indexes. C style is
                        0-based and ordered from slowest
                        iterating dimension to fastest. Fortran
                        style is 1-based and ordered from
                        fastest to slowest iterating dimension
  -l LEN, --length LEN  CDL line length (pncdump only)
  --float-precision FDIG
                        single precision digitis (default 8;
                        pncdump only)
  --double-precision PDIG
                        pdig double precision digits (default
                        16; pncdump only)
  --dump-name CDLNAME   Name for display in ncdump
  --funcs FUNCS         Functions to evaluate split by ,
                        (default: NO,NP,NOP,MO,MP,MdnO,MdnP,STD
                        O,STDP,RM,RMdn,MB,MdnB,WDMB,WDMdnB,FB,M
                        NB,MdnNB,NMB,NMdnB,USUTPB,PSUTMNPB,PSUT
                        MdnNPB,PSUTNMPB,PSUTNMdnPB,ME,MdnE,WDME
                        ,WDMdnE,FE,MNE,MdnNE,NME,NMdnE,USUTPE,P
                        SUTMNPE,PSUTMdnNPE,PSUTNMPE,PSUTNMdnPE,
                        R2,RMSE,RMSEs,RMSEu,E1,IOA,d1,AC,WDIOA,
                        WDRMSE,WDAC)

Detailed Steps
--------------

PseudoNetCDF has many operations and the order often matters. The order is consistent with the order of options in the formatted help. The default order is summarized as:

1. Open with specified reader (-f)
2. Select subset of variables (-v)
2. Add attributes (-a)
4. Apply masks (--mask)
5. Add conventions to support later operations (--to-convention, --from-convention)
6. Combine files via stacking on dimensions (--stack)
7. Slice dimensions (-s --slice)
8. Reduce dimensions (-r --reduce)
9. Convolve dimensions (-c)
10. Extract specific coordinates (--extract)
11. Remove singleton dimensions (--remove-singleton)
12. Apply expressions (--expr then --exprscripts)
13. Apply binary operators (--op_typ)

To impose your own order, use standard options (global options) and then use -- to force positional interpretation of remaining options. In remaining options, use --sep to separate groups of files and options to be evaluated before any global operations.

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