In [2]:
from notebook.services.config import ConfigManager
cfgm = ConfigManager()
cfgm.update('livereveal', {
              'theme': 'simple',
              'transition': 'convex',
              'start_slideshow_at': 'selected'
})


Out[2]:
{'start_slideshow_at': 'selected', 'theme': 'simple', 'transition': 'convex'}

In [ ]:

Python Analysis Evaluation

Author: Barron H. Henderson


In [3]:
# Prepare my slides
%pylab inline
%cd working


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

Process AQS for evaluation

  1. Download annual zip file(s)
  2. Unzip
  3. Use sed, grep, or awk to get spatial/temporal subset
  4. Reshape data
    1. Missing data should be masked
    2. Dimensions (time, point)

CHECK POINT

1. What do you think the dimensions should be for AQS observations?

2. What meta-data should be present?

Getting AQS Observations

  1. Get AQS observations
    1. Raw outputs from AQS website
    2. Representational State Transfer - good for small amounts of data
  2. REST format was having problems due to its transition.

Raw outputs

  1. Download directly or download inline

In [5]:
!pncaqsraw4pnceval.py --help


usage: pncaqsraw4pnceval.py [-h] [--sampleval SAMPLEVAL]
                            [--timeresolution {daily,hourly}]
                            -s BDATE -e EDATE [-r RDATE]
                            [--param [PARAM]]
                            (--gridcro2d GRIDCRO2D | --wktpolygon WKTPOLYGON)
                            [-o [OUTPATH]] [-O]

Converts AQS Raw Hourly files for comparison with pncgen
--extract files. Example Workflow: $ %s --start-date=2006-08-01
--end-date=2012-08-01 --param=44201 GRIDCRO2D_Benchmark $
pncdump --header AQS_DATA_20060801-20060801.nc | grep
lonlatcoords :lonlatcoords =
"-87.881412,30.498001/-85.802182,33.281261/..." ; $ pncgen -s
LAY,0 --extract="-87.881412,30.498001/-85.802182,33.281261/..."
CCTM_V5g_par_Linux2_x86_64gfort.ACONC.CMAQ-BENCHMARK_20060801
Benchmark_20060801-20060801.nc $ pnceval
AQS_DATA_20060801-20060801.nc Benchmark_20060801-20060801.nc

optional arguments:
  -h, --help            show this help message and exit
  --sampleval SAMPLEVAL
                        Defaults to "Sample Measurement" for
                        hourly and "Arithmetic Mean" for daily
  --timeresolution {daily,hourly}
                        Defaults to hourly
  -s BDATE, --start-date BDATE
                        Start date (inclusive) YYYY-MM-DD
  -e EDATE, --end-date EDATE
                        Start date (inclusive) YYYY-MM-DD
  -r RDATE, --ref-date RDATE
                        Reference date YYYYMMDD HH:MM:SS
  --param [PARAM]       Must exist as an AQS parameter
  --gridcro2d GRIDCRO2D
                        CMAQ MCIP GRIDCRO2D file or any file
                        that has LAT and LON variables
  --wktpolygon WKTPOLYGON
  -o [OUTPATH], --output [OUTPATH]
                        Path for output defaults to
                        AQS_DATA_YYYYMMDD-YYYYMMDD.nc.
  -O, --overwrite       Ovewrite if output already exists.

wktpolygon

This option is most relevant for regional extractions.


In [6]:
from shapely.wkt import loads
geom = loads("POLYGON ((30 10, 40 35, 20 40, 10 20, 30 10))")
x, y = geom.exterior.xy
plt.plot(x, y, ls = '-', marker = 'o')


Out[6]:
[<matplotlib.lines.Line2D at 0x10f606fd0>]

CHECK POINT

What should the bounding box be as a WKT Polygon?

ANSWERS Hidden

"POLYGON ((llcrnrlon llcrnrlat, lrcrnrlon lrcrnrlat, urcrnrlon urcrnrlat, ulcrnrlon ulcrnrlat, llcrnrlon llcrnrlat))"

Download and Process


In [8]:
!pncaqsraw4pnceval.py -O --timeresolution=daily \
    --start-date 2013-05-01 --end-date 2013-07-01 \
    --wktpolygon "POLYGON ((-181.25 0, 178.75 0, 178.75 90, -181.25 90, -181.25 0))"


Downloading daily_44201_2013.csv
Reading daily_44201_2013.csv
Concatenating files
Creating output file
Processing data rows
   0%   1%   3%   4%   6%   8%   9%  11%  12%  14%  16%  17%  19%  20%  22%  24%  25%  27%  29%  30%  32%  33%  35%  37%  38%  40%  41%  43%  45%  46%  48%  50%  51%  53%  54%  56%  58%  59%  61%  62%  64%  66%  67%  69%  70%  72%  74%  75%  77%  79%  80%  82%  83%  85%  87%  88%  90%  91%  93%  95%  96%  98%
Writing to disk
Successful

In [9]:
%ls -l AQS_DATA_20130501-20130701.nc


-rw-r--r-- 1 barronh 387658 Jul 15 21:11 AQS_DATA_20130501-20130701.nc

Review Output


In [10]:
!pncdump.py --header AQS_DATA_20130501-20130701.nc


netCDF4._netCDF4.Dataset AQS_DATA_20130501-20130701.nc {
dimensions:
        time = UNLIMITED // (62 currently) 
        LAY = 1 ;
        points = 1295 ;

variables:
        float latitude(points);
                latitude:units = "degrees_north" ;
                latitude:standard_name = "latitude" ;
        float longitude(points);
                longitude:units = "degrees_east" ;
                longitude:standard_name = "longitude" ;
        float Ozone(time, LAY, points);
                Ozone:_FillValue = -999.0 ;
                Ozone:units = "Parts per million" ;
                Ozone:standard_name = "Ozone" ;
        float time(time);
                time:units = "days since 1900-01-01" ;
                time:standard_name = "time" ;


// global properties:
                :SITENAMES = "010030010;010331002;010499991;010510001;010550011;010690004;010730023;010731003;010731005;010731010;010732006;010735003;010736002;010890014;010890022;010970003;010972005;011011002;011030011;011130002;011170004;011190003;011250010;020680003;020900034;040038001;040051008;040058001;040070010;040128000;040130019;040131003;040131004;040131010;040132001;040132005;040133002;040133003;040134003;040134004;040134005;040134008;040134010;040134011;040135100;040137003;040137020;040137021;040137022;040137024;040139508;040139702;040139704;040139706;040139997;040170119;040190021;040191011;040191018;040191020;040191028;040191030;040191032;040191034;040213001;040213003;040213007;040217001;040218001;040258033;040278011;050199991;050350005;051010002;051130003;051190007;051191002;051191008;051430005;051430006;060010007;060010009;060010011;060012001;060050002;060070007;060070008;060090001;060111002;060130002;060131002;060131004;060132007;060170010;060170012;060170020;060190007;060190011;060190242;060192009;060194001;060195001;060210003;060231004;060231005;060250005;060251003;060254004;060270101;060290007;060290008;060290011;060290014;060290232;060292012;060295002;060296001;060310500;060311004;060333001;060370002;060370016;060370113;060371002;060371103;060371201;060371302;060371602;060371701;060372005;060374002;060374006;060375005;060376012;060379033;060390004;060390500;060392010;060410001;060430003;060430006;060470003;060530002;060530008;060531003;060550003;060570005;060570007;060590007;060591003;060592022;060595001;060610003;060610004;060610006;060612002;060650008;060650009;060650012;060650016;060651004;060651010;060651016;060652002;060655001;060656001;060658001;060658005;060659001;060659003;060670002;060670006;060670010;060670011;060670012;060670014;060675003;060690002;060690003;060710001;060710005;060710012;060710306;060711001;060711004;060711234;060712002;060714001;060714003;060719002;060719004;060730001;060730003;060731001;060731002;060731006;060731008;060731010;060731011;060731016;060731201;060732007;060750005;060771002;060773005;060790005;060792006;060793001;060794002;060798001;060798005;060798006;060811001;060830008;060830011;060831008;060831013;060831014;060831018;060831021;060831025;060832004;060832011;060833001;060834003;060850002;060850005;060851001;060852006;060852009;060870007;060871003;060890004;060890007;060890009;060893003;060932001;060950004;060950005;060953003;060970003;060971003;060990005;060990006;061010003;061010004;061030004;061030005;061070006;061070009;061072002;061072010;061090005;061110007;061110009;061111004;061112002;061113001;061130004;061131003;080013001;080050002;080050006;080130011;080150001;080190004;080190005;080310002;080310026;080350004;080410013;080410016;080450012;080450014;080450015;080450017;080450019;080450021;080510008;080519991;080570003;080590005;080590006;080590011;080590013;080671004;080677001;080677003;080690007;080690011;080690012;080691004;080699991;080770020;080770021;080770022;080810002;080830006;080830101;080930001;080970002;081030005;081030006;081130008;081230009;081230011;081230012;090010017;090011123;090013007;090019003;090031003;090050005;090070007;090090027;090099002;090110124;090131001;090159991;100010002;100031007;100031010;100031013;100032004;100051002;100051003;110010041;110010043;110010050;120013011;120030002;120050006;120090007;120094001;120110033;120112003;120118002;120210004;120230002;120310077;120310100;120310106;120330004;120330018;120350004;120550003;120570081;120571035;120571065;120573002;120590004;120619991;120690002;120712002;120713002;120730012;120730013;120779991;120813002;120814012;120814013;120830003;120830004;120860027;120860029;120910002;120950008;120952002;120972002;120990009;120990020;121010005;121012001;121030004;121030018;121035002;121056005;121056006;121130015;121151005;121151006;121152002;121171002;121272001;121275002;121290001;130210012;130510021;130550001;130590002;130670003;130730001;130770002;130850001;130890002;130970004;131210055;131270006;131350002;131510002;132130003;132150008;132230003;132319991;132450091;132470001;132611001;150030010;150031004;160010010;160010017;160230101;170010007;170190007;170191001;170230001;170310001;170310032;170310064;170310076;170311003;170311601;170313103;170314002;170314007;170314201;170317002;170436001;170491001;170650002;170831001;170859991;170890005;170971007;171110001;171132003;171150013;171170002;171190008;171191009;171193007;171199991;171430024;171431001;171570001;171613002;171630010;171670014;171971011;172012001;180030002;180030004;180050007;180110001;180150002;180190008;180350010;180390007;180431004;180550001;180570006;180590003;180630004;180690002;180710001;180810002;180839991;180890022;180890030;180892008;180910005;180910010;180950010;180970050;180970057;180970073;180970078;181090005;181230009;181270024;181270026;181290003;181410010;181410015;181410016;181450001;181630013;181630021;181670018;181670024;181699991;181730008;181730009;181730011;190170011;190450021;190850007;190851101;191130028;191130033;191130040;191370002;191471002;191530030;191630015;191690011;191770006;191810022;200910010;201030003;201070002;201730010;201730018;201770013;201910002;201950001;202090021;210130002;210131002;210150003;210190017;210290006;210373002;210430500;210470006;210590005;210610501;210670012;210890007;210910012;210930006;211010014;211110027;211130001;211390003;211451024;211759991;211850004;211930003;211950002;211990003;212130004;212219991;212270009;212299991;220050004;220150008;220170001;220190002;220190008;220190009;220330003;220330009;220330013;220470009;220470012;220511001;220550007;220570004;220630002;220710012;220730004;220770001;220870004;220890003;220930002;220950002;221030002;221210001;230010014;230031100;230039991;230050029;230052003;230090102;230090103;230112005;230130004;230173001;230194008;230230006;230290019;230290032;230310038;230310040;230312002;240030014;240051007;240053001;240090011;240130001;240150003;240170010;240190004;240199991;240210037;240230002;240251001;240259001;240290002;240313001;240330030;240338003;240339991;240430009;245100054;250010002;250034002;250051004;250051006;250070001;250092006;250094005;250095005;250130008;250150103;250154002;250170009;250213003;250250041;250250042;250270015;250270024;260050003;260190003;260210014;260270003;260330901;260370001;260490021;260492001;260630007;260650012;260770008;260810020;260810022;260910007;260990009;260991003;261010922;261050007;261130001;261210039;261250001;261390005;261470005;261530001;261579991;261610008;261619991;261630001;261630019;261659991;270031001;270031002;270052013;270177416;270353204;270495302;270530962;270750005;270834210;270953051;271095008;271370034;271377550;271390505;271453052;271636016;271713201;280110001;280330002;280450003;280470008;280490010;280490020;280590006;280750003;280810005;281619991;290030001;290190011;290270002;290370003;290390001;290470003;290470005;290470006;290490001;290770036;290770042;290970004;290990019;291130003;291370001;291570001;291831002;291831004;291860005;291890005;291890014;292130004;295100085;300270006;300298001;300490004;300630024;300710010;300750001;300830001;300870001;310550019;310550028;310550035;311079991;311090016;320010002;320030022;320030023;320030043;320030071;320030073;320030075;320030538;320030540;320030601;320031019;320032002;320038000;320190006;320310016;320310020;320310025;320311005;320312002;320312009;320330101;325100020;330012004;330050007;330074001;330074002;330090010;330099991;330111011;330115001;330131007;330150014;330150016;330150018;340010006;340030006;340070002;340071001;340110007;340130003;340150002;340170006;340190001;340210005;340219991;340230011;340250005;340273001;340290006;340315001;340410007;350010023;350010024;350010027;350010029;350010032;350011012;350011013;350130008;350130017;350130020;350130021;350130022;350130023;350151005;350153001;350171003;350250008;350290003;350390026;350431001;350450009;350450018;350451005;350490021;350610008;360010012;360050110;360050133;360130006;360270007;360290002;360310002;360310003;360319991;360337003;360410005;360430005;360450002;360551007;360610135;360631006;360671015;360715001;360750003;360790005;360810124;360850067;360870005;360910004;361010003;361030002;361030004;361030009;361099991;361173001;361192004;370030004;370110002;370119991;370210030;370270003;370319991;370330001;370370004;370510008;370511003;370590003;370630015;370650099;370670022;370670028;370670030;370671008;370690001;370750001;370770001;370810013;370870008;370870035;370870036;370990005;371010002;371070004;371090004;371139991;371170001;371190041;371191005;371191009;371239991;371290002;371450003;371470006;371570099;371590021;371590022;371730002;371730007;371790003;371830014;371830016;371990004;380070002;380130004;380150003;380171004;380250003;380530002;380570004;380650002;381050003;390030009;390071001;390170004;390170018;390179991;390230001;390230003;390250022;390271002;390350034;390350060;390350064;390355002;390410002;390479991;390490029;390490037;390490081;390550004;390570006;390610006;390610010;390610040;390810017;390830002;390850003;390850007;390870011;390870012;390890005;390930018;390950024;390950027;390950034;390970007;390990013;391030004;391090005;391130037;391219991;391331001;391351001;391510016;391510022;391514005;391530020;391550009;391550011;391650007;391670004;391730003;400019009;400159008;400170101;400219002;400270049;400310651;400370144;400430860;400670671;400719010;400850300;400871073;400979014;401090033;401090096;401091037;401159004;401210415;401259023;401359021;401430137;401430174;401430178;401431127;410050004;410090004;410170122;410290201;410390060;410391007;410470004;410510080;410591003;410671004;420019991;420030008;420030010;420030067;420031005;420050001;420070002;420070005;420070014;420110006;420110011;420130801;420150011;420170012;420210011;420270100;420279991;420290100;420334000;420430401;420431100;420450002;420479991;420490003;420550001;420590002;420630004;420690101;420692006;420710007;420710012;420730015;420750100;420770004;420791100;420791101;420810100;420850100;420859991;420890002;420910013;420950025;420958000;420990301;421010004;421010024;421011002;421119991;421174000;421250005;421250200;421255001;421255200;421290006;421290008;421330008;421330011;440030002;440071010;440090007;450010001;450030003;450070005;450150002;450190046;450210002;450210003;450250001;450290002;450310003;450370001;450450016;450451003;450730001;450770002;450770003;450790007;450790021;450791001;450830009;450910006;450918001;450918002;460110003;460330132;460710001;460930001;460990008;461270001;470010101;470090101;470090102;470259991;470370011;470370026;470419991;470651011;470654003;470890002;470930021;470931020;471050109;471210104;471550101;471550102;471570021;471570075;471571004;471632002;471632003;471650007;471870106;471890103;480271047;480290032;480290052;480290059;480391004;480391016;480430101;480610006;480611023;480850005;481130069;481130075;481130087;481210034;481211032;481390016;481391044;481410029;481410037;481410044;481410055;481410057;481410058;481671034;481830001;482010024;482010026;482010029;482010046;482010047;482010051;482010055;482010062;482010066;482010075;482010416;482011015;482011017;482011034;482011035;482011039;482011050;482030002;482150043;482210001;482311006;482450009;482450011;482450022;482450101;482450102;482450628;482451035;482510003;482570005;483091037;483390078;483491051;483550025;483550026;483611001;483611100;483670081;483739991;483819991;483970001;484230007;484390075;484391002;484392003;484393009;484393011;484530014;484530020;484690003;484790016;490030003;490037001;490050004;490071003;490090001;490110004;490130002;490131001;490137011;490170004;490352004;490353006;490370101;490450003;490470014;490471002;490471003;490472002;490472003;490475632;490477022;490490002;490495010;490530007;490530130;490570002;490571003;500030004;500070007;510030001;510130020;510330001;510360002;510410004;510590030;510610002;510690010;510719991;510850003;510870014;511071005;511130003;511390004;511479991;511530009;511611004;511630003;511650003;511790001;511970002;515100021;516500008;518000004;518000005;530090013;530110011;530330010;530330017;530330023;530330080;530530012;530531010;530570011;530570020;530630001;530630021;530630046;530670005;530730005;540030003;540110006;540219991;540250003;540291004;540390010;540610003;540690010;540939991;541071002;550030010;550090026;550210015;550250041;550270001;550290004;550350014;550390006;550410007;550550009;550590019;550590025;550610002;550630012;550710007;550730012;550790010;550790026;550790085;550870009;550890008;550890009;551010017;551050024;551110007;551170006;551199991;551250001;551270005;551330027;560019991;560030002;560050123;560050456;560070100;560090801;560130099;560130232;560136001;560210100;560250100;560252601;560330004;560350097;560350099;560350100;560350101;560350700;560351002;560359991;560370077;560370100;560370200;560370300;560390008;560391011;560410101;560450003;720330008;720770001;800020003;800060004;800060006;800060007" ;
                :lonlatcoords = 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;
}

Extract GEOS-Chem at AQS


In [11]:
!pncgen -O -f "bpch,vertgrid='GEOS-5-NATIVE',nogroup=('IJ-AVG-$',)" \
        --extract-file AQS_DATA_20130501-20130701.nc --stack=time -v O3 -s layer72,0 \
        bpch/ctm.bpch.v10-01-public-Run0.2013050100 \
        bpch/ctm.bpch.v10-01-public-Run0.2013050100 \
        bpch_aqs_extract.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 [12]:
!pncdump.py --header bpch_aqs_extract.nc


netCDF4._netCDF4.Dataset bpch_aqs_extract.nc {
dimensions:
        time = 2 ;
        layer72 = 1 ;
        latitude = 46 ;
        longitude = 72 ;
        layer = 72 ;
        layer_bounds = 73 ;
        tnv = 2 ;
        nv = 2 ;
        points = 1295 ;

variables:
        float O3(time, layer72, points);
                O3:coordinates = "time layer72 latitude longitude" ;
                O3:category = "IJ-AVG-$" ;
                O3:carbon = 1 ;
                O3:kgpermole = 0.048000000000000001 ;
                O3:units = "ppbv" ;
                O3:standard_name = "O3" ;
                O3:grid_mapping = "crs" ;
                O3:scale = True ;
                O3:base_units = "                                        " ;
                O3:reserved = "                                        " ;
                O3:tracerid = 2 ;
                O3:var_desc = "O3" ;
                O3:long_name = "O3" ;
        double time(time);
                time:base_units = "hours since 1985-01-01 00:00:00 UTC" ;
                time:units = "hours since 1985-01-01 00:00:00 UTC" ;
                time:bounds = "time_bounds" ;
                time:var_desc = "time" ;
                time:standard_name = "time" ;
                time:long_name = "time" ;
                time:coordinates = "time" ;
        double longitude(points);
                longitude:base_units = "degrees_east" ;
                longitude:units = "degrees_east" ;
                longitude:bounds = "longitude_bounds" ;
                longitude:standard_name = "longitude" ;
                longitude:axis = "X" ;
                longitude:long_name = "longitude" ;
                longitude:coordinates = "longitude" ;
        float layer(layer);
                layer:positive = "up" ;
                layer:standard_name = "hybrid_sigma_pressure" ;
                layer:units = "level" ;
                layer:long_name = "hybrid level at layer midpoints" ;
                layer:coordinates = "layer" ;
        double etai_pressure(layer_bounds);
                etai_pressure:base_units = "hPa" ;
                etai_pressure:units = "hPa" ;
                etai_pressure:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ;
                etai_pressure:var_desc = "etai_pressure" ;
                etai_pressure:long_name = "etai_pressure" ;
                etai_pressure:coordinates = "layer_bounds" ;
        double time_bounds(time, tnv);
                time_bounds:base_units = "hours since 1985-01-01 00:00:00 UTC" ;
                time_bounds:units = "hours since 1985-01-01 00:00:00 UTC" ;
                time_bounds:standard_name = "time_bounds" ;
                time_bounds:var_desc = "time_bounds" ;
                time_bounds:long_name = "time_bounds" ;
                time_bounds:coordinates = "time tnv" ;
        double longitude_bounds(points, nv);
                longitude_bounds:base_units = "degrees_east" ;
                longitude_bounds:units = "degrees_east" ;
                longitude_bounds:standard_name = "longitude" ;
                longitude_bounds:axis = "X" ;
                longitude_bounds:long_name = "longitude" ;
                longitude_bounds:coordinates = "longitude nv" ;
        double latitude_bounds(points, nv);
                latitude_bounds:base_units = "degrees_north" ;
                latitude_bounds:units = "degrees_north" ;
                latitude_bounds:standard_name = "latitude" ;
                latitude_bounds:axis = "Y" ;
                latitude_bounds:long_name = "latitude" ;
                latitude_bounds:coordinates = "latitude nv" ;
        float layer72(layer72);
                layer72:positive = "up" ;
                layer72:standard_name = "hybrid_sigma_pressure" ;
                layer72:units = "level" ;
                layer72:long_name = "hybrid level at layer midpoints" ;
                layer72:coordinates = "layer72" ;
        double latitude(points);
                latitude:base_units = "degrees_north" ;
                latitude:units = "degrees_north" ;
                latitude:bounds = "latitude_bounds" ;
                latitude:standard_name = "latitude" ;
                latitude:axis = "Y" ;
                latitude:long_name = "latitude" ;
                latitude:coordinates = "latitude" ;
        double etam_pressure(layer);
                etam_pressure:base_units = "hPa" ;
                etam_pressure:units = "hPa" ;
                etam_pressure:standard_name = "atmosphere_hybrid_sigma_pressure_coordinate" ;
                etam_pressure:var_desc = "etam_pressure" ;
                etam_pressure:long_name = "etam_pressure" ;
                etam_pressure:coordinates = "layer" ;
        float layer_bounds(layer_bounds);
                layer_bounds:positive = "up" ;
                layer_bounds:standard_name = "hybrid_sigma_pressure" ;
                layer_bounds:units = "level" ;
                layer_bounds:long_name = "hybrid level at layer midpoints" ;
                layer_bounds:coordinates = "layer_bounds" ;


// global properties:
                :noscale = 0 ;
                :nogroup = "IJ-AVG-$" ;
                :ftype = "CTM bin 02                              " ;
                :toptitle = "GEOS-CHEM binary punch file v. 2.0                                              " ;
                :modelname = "GEOSFP              " ;
                :modelres = array([  5.74868682e-41,   4.60074312e-41], dtype=float32) ;
                :halfpolar = 1 ;
                :center180 = 1 ;
                :start_tau0 = 248328.0 ;
                :start_tau1 = 249072.0 ;
                :vertgrid = "GEOS-5-NATIVE" ;
                :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,   6.66034100e+01,   5.63879100e+01,
         4.76439100e+01,   4.01754100e+01,   3.38100100e+01,
         2.83678100e+01,   2.37304100e+01,   1.97916000e+01,
         1.64571000e+01,   1.36434000e+01,   1.12769000e+01,
         9.29294200e+00,   7.61984200e+00,   6.21680100e+00,
         5.04680100e+00,   4.07657100e+00,   3.27643100e+00,
         2.62021100e+00,   2.08497000e+00,   1.65079000e+00,
         1.30051000e+00,   1.01944000e+00,   7.95134100e-01,
         6.16779100e-01,   4.75806100e-01,   3.65041100e-01,
         2.78526100e-01,   2.11349000e-01,   1.59495000e-01,
         1.19703000e-01,   8.93450200e-02,   6.60000100e-02,
         4.75850100e-02,   3.27000000e-02,   2.00000000e-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,
         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,   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/src/PseudoNetCDF/pncgen.py -O -f bpch,vertgrid="GEOS-5-NATIVE",nogroup=("IJ-AVG-$",) --extract-file AQS_DATA_20130501-20130701.nc --stack=time -v O3 -s layer72,0 bpch/ctm.bpch.v10-01-public-Run0.2013050100 bpch/ctm.bpch.v10-01-public-Run0.2013050100 bpch_aqs_extract.nc;/Users/barronh/Development/pseudonetcdf/src/PseudoNetCDF/pncgen.py -O -f bpch,vertgrid="GEOS-5-NATIVE",nogroup=("IJ-AVG-$",) --extract-file AQS_DATA_20130501-20130701.nc --stack=time -v O3 -s layer72,0 bpch/ctm.bpch.v10-01-public-Run0.2013050100 bpch/ctm.bpch.v10-01-public-Run0.2013050100 bpch_aqs_extract.nc;slice_dim(f, layer72,0, fuzzydim = True); " ;
                :lonlatcoords = 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;
}

In [13]:
!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.

In [14]:
%%bash
pnceval.py --funcs NO,NP,NOP,MO,MP,MB,RMSE,IOA,AC -v O3 \
--pnc " --expr O3=Ozone*1000;O3.units=\'ppb\' -r time,mean AQS_DATA_20130501-20130701.nc" \
--pnc " -r time,mean bpch_aqs_extract.nc"


AQS_DA_0 = ifile0 = AQS_DATA_20130501-20130701.nc
bpch_a_0 = ifile1 = bpch_aqs_extract.nc
2013-05-31 12:00:00,2013-05-31 12:00:00,O3,N Observations (#),NO,1295.000000
2013-05-31 12:00:00,2013-05-31 12:00:00,O3,N Predictions (#),NP,1295.000000
2013-05-31 12:00:00,2013-05-31 12:00:00,O3,N Observations/Prediction Pairs (#),NOP,1295.000000
2013-05-31 12:00:00,2013-05-31 12:00:00,O3,Mean Observations (obs unit),MO,34.267725
2013-05-31 12:00:00,2013-05-31 12:00:00,O3,Mean Predictions (model unit),MP,43.995331
2013-05-31 12:00:00,2013-05-31 12:00:00,O3,Mean Bias,MB,9.727605
2013-05-31 12:00:00,2013-05-31 12:00:00,O3,Root Mean Square Error (model unit),RMSE,11.633646
2013-05-31 12:00:00,2013-05-31 12:00:00,O3,Index of Agreement, IOA,IOA,0.502660
2013-05-31 12:00:00,2013-05-31 12:00:00,O3,Anomaly Correlation,AC,0.146968
**PNC:/Users/barronh/Development/pseudonetcdf/src/PseudoNetCDF/pnceval.py:371:UserWarning:
  Assumes input order is obs model

In [15]:
from PseudoNetCDF import pnceval
help(pnceval)


Help on module PseudoNetCDF.pnceval in PseudoNetCDF:

NAME
    PseudoNetCDF.pnceval

FUNCTIONS
    AC(obs, mod, axis=None)
        Anomaly Correlation
    
    E1(obs, mod, axis=None)
        Modified Coefficient of Efficiency, E1
    
    FB(obs, mod, axis=None)
        Fractional Bias (%)
    
    FE(obs, mod, axis=None)
        Fractional Error (%)
    
    IOA(obs, mod, axis=None)
        Index of Agreement, IOA
    
    MB(obs, mod, axis=None)
        Mean Bias
    
    ME(obs, mod, axis=None)
        Mean Gross Error (model and obs unit)
    
    MNB(obs, mod, axis=None)
        Mean Normalized Bias (%)
    
    MNE(obs, mod, axis=None)
        Mean Normalized Gross Error (%)
    
    MO(obs, mod, axis=None)
        Mean Observations (obs unit)
    
    MP(obs, mod, axis=None)
        Mean Predictions (model unit)
    
    MdnB(obs, mod, axis=None)
        Median Bias
    
    MdnE(obs, mod, axis=None)
        Median Gross Error (model and obs unit)
    
    MdnNB(obs, mod, axis=None)
        Median Normalized Bias (%)
    
    MdnNE(obs, mod, axis=None)
        Median Normalized Gross Error (%)
    
    MdnO(obs, mod, axis=None)
        Median Observations (obs unit)
    
    MdnP(obs, mod, axis=None)
        Median Predictions (model unit)
    
    NMB(obs, mod, axis=None)
        Normalized Mean Bias (%)
    
    NME(obs, mod, axis=None)
        Normalized Mean Error (%)
    
    NMdnB(obs, mod, axis=None)
        Normalized Median Bias (%)
    
    NMdnE(obs, mod, axis=None)
        Normalized Median Error (%)
    
    NO(obs, mod, axis=None)
        N Observations (#)
    
    NOP(obs, mod, axis=None)
        N Observations/Prediction Pairs (#)
    
    NP(obs, mod, axis=None)
        N Predictions (#)
    
    PSUTMNPB(obs, mod, axis=None)
        Paired Space/Unpaired Time Mean Normalized Peak Bias (%)
    
    PSUTMNPE(obs, mod, axis=None)
        Paired Space/Unpaired Time Mean Normalized Peak Error (%)
    
    PSUTMdnNPB(obs, mod, axis=None)
        Paired Space/Unpaired Time Median Normalized Peak Bias (%)
    
    PSUTMdnNPE(obs, mod, axis=None)
        Paired Space/Unpaired Time Median Normalized Peak Error (%)
    
    PSUTNMPB(obs, mod, axis=None)
        Paired Space/Unpaired Time Normalized Mean Peak Bias (%)
    
    PSUTNMPE(obs, mod, axis=None)
        Paired Space/Unpaired Time Normalized Mean Peak Error (%)
    
    PSUTNMdnPB(obs, mod, axis=None)
        Paired Space/Unpaired Time Normalized Median Peak Bias (%)
    
    PSUTNMdnPE(obs, mod, axis=None)
        Paired Space/Unpaired Time Normalized Median Peak Error (%)
    
    R2(obs, mod, axis=None)
        Coefficient of Determination (unit squared)
    
    RM(obs, mod, axis=None)
        Mean Ratio Observations/Predictions (none)
    
    RMSE(obs, mod, axis=None)
        Root Mean Square Error (model unit)
    
    RMSEs(obs, mod, axis=None)
        Root Mean Squared Error systematic (obs, mod_hat)
    
    RMSEu(obs, mod, axis=None)
        Root Mean Squared Error unsystematic (mod_hat, mod)
    
    RMdn(obs, mod, axis=None)
        Median Ratio Observations/Predictions (none)
    
    STDO(obs, mod, axis=None)
        Standard deviation of Observations
    
    STDP(obs, mod, axis=None)
        Standard deviation of Predictions
    
    USUTPB(obs, mod, axis=None)
        Unpaired Space/Unpaired Time Peak Bias (%)
    
    USUTPE(obs, mod, axis=None)
        Unpaired Space/Unpaired Time Peak Error (%)
    
    WDAC(obs, mod, axis=None)
        Wind Direction Anomaly Correlation
    
    WDIOA(obs, mod, axis=None)
        Wind Direction Index of Agreement, IOA
    
    WDMB(obs, mod, axis=None)
        Wind Direction Mean Bias
    
    WDME(obs, mod, axis=None)
        Wind Direction Mean Gross Error (model and obs unit)
    
    WDMdnB(obs, mod, axis=None)
        Wind Direction Median Bias
    
    WDMdnE(obs, mod, axis=None)
        Wind Direction Median Gross Error (model and obs unit)
    
    WDRMSE(obs, mod, axis=None)
        Wind Direction Root Mean Square Error (model unit)
    
    d1(obs, mod, axis=None)
        Modified Index of Agreement, d1

DATA
    __all__ = ['NO', 'NP', 'NOP', 'MO', 'MP', 'MdnO', 'MdnP', 'STDO', 'STD...

FILE
    /Users/barronh/Development/pseudonetcdf/src/PseudoNetCDF/pnceval.py


Reproduced in Python

  1. Read in files
  2. Get variables
  3. Calculate MB, RMSE
  4. Modify
    • Repeat except for month specific results
    • Repeat except for site specific results

Reproduction Provided


In [16]:
from PseudoNetCDF import PNC, pnceval

aqs = PNC("--reduce=time,mean", "--expr=O3=Ozone*1000", "AQS_DATA_20130501-20130701.nc")
geos = PNC("--reduce=time,mean", "bpch_aqs_extract.nc")
aqso3 = aqs.ifiles[0].variables['O3']
geoso3 = geos.ifiles[0].variables['O3']
print(aqso3.shape)
print(geoso3.shape)
print(pnceval.RMSE(aqso3, geoso3))


(1, 1, 1295)
(1, 1, 1295)
11.63364572321664

ANSWERS Hidden

``` from PseudoNetCDF import PNC, pnceval aqs = PNC("--expr=O3=Ozone*1000", "AQS_DATA_20130501-20130701.nc") geos = PNC("bpch_aqs_extract.nc") aqso3 = aqs.ifiles[0].variables['O3'].reshape(2, 31, 1, 1295).mean(1) geoso3 = geos.ifiles[0].variables['O3'] print(aqso3.shape) print(geoso3.shape) print(pnceval.RMSE(aqso3, geoso3, axis = 2)) ```

In [ ]: