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 [ ]:
In [3]:
# Prepare my slides
%pylab inline
%cd working
Populating the interactive namespace from numpy and matplotlib
/Users/barronh/Downloads/GCandPython/working
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.
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>]
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
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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;
}
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
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
In [ ]:
Content source: barronh/GCandPython
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