Numbriliste 4D andmete esmane töötlemine

4D võrguandmed (gridded data)

Formaadid:“uurija” formaatGRIBNetCDF

GRIB ekstraheeriminewgrib SURFER .GRD

Esmane töötlemine GRADS

ÜlesandedKaardid HIROMB andmetest

wgribGRADS

Jüri Elken &Priidik Lagemaa

Okeanograafiliste andmete iseloom

üldjuhul juhuslikud väljad ψ(x,y,z,t)

erijuhud:

1D aegrida ψ(x0 ,y0 ,z0 ,t)1D sügavusprofiil ψ(x0 ,y0 ,z,t0 )1D horisontaalprofiil ψ(x,y0 ,z0 ,t0 )

ψ(x0 ,y,z0 ,t0 )

2D horisontaalne kaart ψ(x,y,z0 ,t0 )2D aeg-sügavuslõige ψ(x0 ,y0 ,z,t)2D ruumiline lõige ψ(x,y0 ,z,t0 )

ψ(x0 ,y,z,t0 )

Esitus: funktsiooni

graafik

Esitus: kaart

Võrguandmed (gridded data)

x, y, z, t diskreetsete sammudega

Erivariandid x, y:tasapinnaline x,y (sh pööratud)Lat, Lon (sh pööratud)ortogonaalne kõverjooneline (Lat, Lon on selle erijuht)

Erivariandid z:sügavused/kihid (sageli muutuva kihi paksusega)sigma-koordinaat (jälgib sügavusi võrdsete vahedega)isopükniline (jälgib liikuvaid samatiheduspindasid)hübriidne (eelnevate kombinatsioon)

vt ka http://www.msi.ttu.ee/~elken/SOL_07.ppthttp://www.msi.ttu.ee/~elken/OceanLim_Notes15.pdf

“uurija” formaat

Uurija kirjutab ise näiteks FORTRANis talle sobivas formaadis ja loeb hiljem samal kujul sisse

Kirjutamisel ja lugemisel tuleb üldjuhul kasutada täpselt samasugust andmete kirjeldust

Tavaliselt puudub info andmete sisu ja aja kohta (selle saab panna küll faili nimesse) ning füüsilise/geograafilise ruumi kohta

Jälgi kas fail on BIG või LITTLE ENDIAN!!! (windows on little-endian)

DIMENSION T(200,200,10)!…..arvutusedOPEN(20,’andmed.dat’, FORM=‘BINARY’)WRITE(20) TCLOSE(20)END

DIMENSION T(200,200,10)

OPEN(20,’andmed.dat’, FORM=‘BINARY’)READ(20) TCLOSE(20)

!…..arvutusedEND

Programmide näited:

GRIB (GRIdded Binary)

GRIB (GRIdded Binary) is a mathematically concise data format commonly used in meteorology to store historical and forecasted weather data. It is standardized by the World Meteorological Organization’s Commission for Basic Systems, known under number GRIB FM 92-IX, described in WMO Manual on Codes No.306. Currently there are two versions of GRIB, first edition (current sub-version is 2) is used operationaly world-wide by all meteorological centers, for Numerical Weather Prediction output (NWP). A newer generation was introduced, known as GRIB second edition, but it is used only by few centers and in many cases not for operational broadcast. Some of the second-generation GRIB are used for derived product distributed in Eumetcast of Meteosat Second Generation.

GRIB superseded the Aeronautical Data Format (ADF).

wikipedia

GRIB 1 Section 0: Indicator Section. GRIB kirje alguse tähis ja pikkusSection 1: Product Definition Section (PDS). Standardsed definitsioonid kodeerituna (võrk, parameeter, aeg, väljaandja jne)Section 2: Grid Description Section (GDS) - Optional. Mittestandardsed definitsioonid. Kasutatakse juhul kui andmed ei ole PDS tabelitega kirjeldatavadSection 3: Bit Map Section (BMS) - Optional. Kasutatakse nt maa punktide märkimiseks so märgitakse ära millistes võrgusõlmedes on olemas andmedSection 4: Binary Data Section (BDS). Andmete pikkus ja andmedSection 5: '7777' - ASCII Characters indicating end of GRID record. Märgib kirje lõppu

GRIB FormaatGRIB Fail koosneb erinevatest kirjetest, mis kõik on isekirjelduvad.

Iga kirje (nt temperatuuri, veetaseme jne väli) koosneb sektsioonidest.

‘GR

IB’

PDS GDS BMS BDS

‘7777’

‘GR

IB’

PDS GDS BMS BDS

‘7777’

2 kirjega GRIB fail

1. kirje 2. kirje

Koodid PDS-is

Parameter-nummer

Parameter Enhet KommentarDef. införd datum

130Skin velocity, x-component

cm/s

131Skin velocity, y-component

cm/s

200 Turbulent Kinetic Energy J/kg

201Dissipation rate of the Turbulent Kinetic Energy

W/kg

202 Eddy viscosity m2/s203 Eddy diffusivity m2/s220 Level ice thickness m221 Ridged ice thickness m222 Ice ridge height m223 Ice ridge density 1/km

GRIB formaadi iseärasusi

+• Isekirjeldav, äärmiselt kokku pakitud kiire andmeülekande jaoks. • Väga paindlik.• Operatiivses okeanograafias ja meteoroloogias üldlevinud standard.

-•4D esituse asemel domineerib 2D, kus ühel ajahetkel on 3D väljad kirjutatud 2D väljade vahelduvaks jadaks.• Orienteeritud meteoandmetele. Mereprognooside puhul tehakse muudatused (üledefineerimised), mis lihtsate programmide juures ei toimi. Ka keerukama softi puhul esinevad konverteerimisel sageli tõrked.• Saadaval WINDOWS tarkvara (nt OCENS GRIB Explorer) mereprognooside faile ei ava.• Kaasaegsete tehnoloogiate (nt openDAP) tugi on nõrk

Only decoders/encoders

•WGRIB and WGRIB2 •Convsh•CDO•Picogrib•NCEP codes •JGrib •Meteosatlib•PyNIO •degrib•GRIB API•GRIB Java Decoder•GDAL•PyGrib

GRIB Software

Viewers

•GrADS•Xconv•NCAR Command Language (linux)•Ugrib•SmartMet•OpenCPN•Panoply

Okeanograafias kasutatav GRIB tarkvara

•WGRIB – Command line based program to manipulate, inventory and decode GRIB files

•GrADS – Linux/Unix based desktop application that handles GRIB •Xconv/Convsh – Xconv is a graphical tool for displaying and converting gridded data, and is available for most operating systems. Convsh is the command-line equivalent.

•CDO (Climate Data Operators) is an analysis tool for geoscientific data with GRIB support

•Panoply netCDF, HDF and GRIB Data Viewer. With Panoply 4 you can do a lot of data manipulations and graphical presentationshttp://www.giss.nasa.gov/tools/panoply/

Töötab hästi erinevate Läänemere andmete jaoks

NetCDF (Network Common Data Form) is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. The project homepage is hosted by the Unidata program at the University Corporation for Atmospheric Research (UCAR). The format is an open standard. NetCDF Classic and 64-bit Offset Format are an international standard of the Open Geospatial Consortium.

The project is actively supported by UCAR. The recently released (2008) version 4.0 greatly enhances the data model by allowing the use of the HDF5 data file format. Version 4.1 (2010) adds support for C and Fortran client access to specified subsets of remote data via OPeNDAP.

The format was originally based on the conceptual model of the NASA CDF but has since diverged and is not compatible with it.

wikipedia

NetCDF (Network Common Data Form)

The freely available distribution contains the C/C++/F77/F90 libraries, (plus tools ncgen/ncdump) and can be obtained as source code as a gzipped tar file or compressed tar file, or see our list of precompiled binaries on the netCDF 3.6.2 downloads page.

http://www.unidata.ucar.edu/software/netcdf/

+• orienteeritud 4D andmetele• võimalikud suured failid üle 2 GB• palju “lehitsejaid”• OpenDAP tugi• suhteliselt lihtne siduda programmeerimiskeeltega (FORTRAN, C, MATLAB, PYTHON jne) • HDF5 tugi

-• Üldlevinud (NetCDF-3) andmete maht (väga) palju suurem kui GRIBil• NetCDF-4/HDF5 andmete maht mõistlik kuid veel ebastabiilne

NetCDF formaadi iseärasusi

netcdf dataset-hbmV2PHYS-bal-latestforecast_1352145534043 {dimensions:

time = 3 ;lat = 70 ;lon = 107 ;depth = 21 ;

variables:int time(time) ;

time:standard_name = "time" ;time:long_name = "time" ;time:units = "hours since 2012-11-05 12:00:00 UTC" ;time:axis = "t" ;time:_CoordinateAxisType = "Time" ;time:valid_min = 25 ;time:valid_max = 27 ;

float lon(lon) ;lon:standard_name = "longitude" ;lon:long_name = "longitude" ;lon:units = "degrees_east" ;lon:unit_long = "Degrees East" ;lon:axis = "x" ;lon:_CoordinateAxisType = "Lon" ;lon:valid_min = 21.4583f ;lon:valid_max = 30.2917f ;

NetCDF faili päisfloat temp(time, depth, lat, lon) ;temp:_CoordinateAxes = "time depth lat lon" ;temp:standard_name = "sea_water_temperature" ;temp:long_name = "potential temperature" ;temp:units = "degree_Celsius" ;temp:unit_long = "degree Celsius" ;temp:valid_range = -3.00000f, 40.0000f ;temp:_FillValue = -999.000f ;temp:missing_value = -999.000f ;

// global attributes::title = "MyOcean Baltic MFC: Physical forecast":institution = "Baltic MFC“:references = "http://ocean.dmi.dk":source = "HBM_V2 model output converted to NetCDF":Conventions = "CF-1.0":time_min = 25.0000 ;:time_max = 27.0000 ;:julian_day_unit = "hours since 2012-11-05 12:00:00

UTC":z_min = 0.000000 ;:z_max = 100.000 ;:latitude_min = 56.5250 ;:latitude_max = 59.9750 ;:longitude_min = 21.4583 ;:longitude_max = 30.2917 ;

}

mõõtmed

muutu

jad

üldinfo

OpenDAP – the cloud framework for scientific data

OPeNDAP is a framework that simplifies all aspects of scientific data networking.

OPeNDAP provides software which makes local data accessible to remote locations regardless of local storage format.

OPeNDAP also provides tools for transforming existing applications into OPeNDAP clients (i.e., enabling them to remotely access OPeNDAP served data).

OPeNDAP software is freely available.http://www.opendap.org/

Test openDAP interface athttp://test.opendap.org/dap/data/nc/

The THREDDS Data Server (TDS) is a web server that provides metadata and data access for scientific datasets, using OPeNDAP, OGC WMS and WCS, HTTP, and other remote data access protocols.

ODV – the interactive exploration of scientific data

Ocean Data View (ODV) is a software package for the interactive exploration, analysis and visualization of oceanographic and other geo-referenced profile, time-series, trajectory or sequence data.

The ODV data format allows dense storage and very fast data access. Large data collections with millions of stations can easily be maintained and explored on  inexpensive desktop and notebook computers. Data from ARGO, GTSPP, CCHDO,  World Ocean Database, World Ocean Atlas, World Ocean Circulation Experiment (WOCE), SeaDataNet, and Medar/Medatlas can be directly imported into ODV.

ODV also supports the netCDF format and lets you explore and visualize CF, COARDS, GDT and CDC compliant netCDF datasets. This works with netCDF files on your local machine as well as with remote netCDF files served by an OPeNDAP server. 

http://odv.awi.de/en/home/

Test nc file athttp://www.msi.ttu.ee/~priidik.lagemaa/NSO8054/

ODV – Ocean Data View (Reiner Schlizer) http://odv.awi.de

Otsi ja lae internetist allawgrib.execygwin1.dll

TeeRun cmdja siis DOS aknaswgrib

wgribhttp://www.cpc.ncep.noaa.gov/products/wesley/wgrib.html

Kiiremaks navigeerimiseks käsureal kasuta Tab klahvi!!!

Laadi wgrib kataloogi loengumaterjalide hulgastBS01_200709040000+000H00M. Vaatame faili sisu:

Ülesanne 1 (1)Kirje number

Kirje alguse asukoht failis (bait)

Kuupäev

Parameetri lühend

Kõrgus/sügavus

KIRJE SISU TABELIST!!!

Kust kõrgus mõõdetud

Kõrgus/sügavus

Ekstraheerime kirje 16 (temperatuur veepinnal, vt eelmine slaid) tekstifaili

punkte x ja y suunas

tühik (andmete puudumine)

Ülesanne 1 (2)

Teisenda 1D tekstifail temp.dat SURFER 2D failiks temp.grd

Laadi wgrib kataloogi loengumaterjalide hulgasttxt2grd.exe ja DOS aknas teetxt2grd temp.dat

txt2grd.for! Converts Text output from wgrib to 2D SURFER binary GRD file! To add geographical reference, save in SURFER as ASCII file and edit bounds! by Jüri Elken! Usage: txt2grd input.xxx! Output file is input.grd

Ekstraheeri mõni teine kirje/väli ja joonista kaart Eesti rannikumeres

Geograafiliste koordinaatide määramiseks tee:

wgrib bs01 -V

DSAA752 7350 7510 7346.0172600746155 18.613899230957

GRD ASCII formaadis asenda:

http://badc.nerc.ac.uk/help/software/xconv/

Xconv“kiireks” sirvimiseks ja konverteerimiseks

Xconv is an program designed to convert model output into a format suitable for use in various plotting packages. Xconv is designed to be simple to use with a point and click, X-windows based interface. Xconv can read data in the following formats: •Data output from the UKMO Unified Model •UKMO PP format •GRIB format •Netcdf format •Drs format

The following output formats are supported by xconv: •Netcdf format •Drs format •Utf format

http://grads.iges.org/grads/

Grid Analysis and Display System (GrADS)

The Grid Analysis and Display System (GrADS) is an interactive desktop tool that is used for easy access, manipulation, and visualization of earth science data. The format of the data may be either binary, GRIB, NetCDF, or HDF-SDS (Scientific Data Sets). GrADS has been implemented worldwide on a variety of commonly used operating systems and is freely distributed over the Internet.

GrADS uses a 4-Dimensional data environment: longitude, latitude, vertical level, and time. Data sets are placed within the 4-D space by use of a data descriptor file. GrADS interprets station data as well as gridded data, and the grids may be regular, non-linearly spaced, gaussian, or of variable resolution. Data from different data sets may be graphically overlaid, with correct spatial and time registration. Operations are executed interactively by entering FORTRAN-like expressions at the command line. A rich set of built-in functions are provided, but users may also add their own functions as external routines written in any programming language.

Center for Ocean-Land-Atmosphere Studies

Data may be displayed using a variety of graphical techniques: line and bar graphs, scatter plots, smoothed contours, shaded contours, streamlines, wind vectors, grid boxes, shaded grid boxes, and station model plots. Graphics may be output in PostScript or image formats. GrADS provides geophysically intuitive defaults, but the user has the option to control all aspects of graphics output.

GrADS has a programmable interface (scripting language) that allows for sophisticated analysis and display applications. Use scripts to display buttons and dropmenus as well as graphics, and then take action based on user point-and-clicks. GrADS can be run in batch mode, and the scripting language facilitates using GrADS to do long overnight batch jobs.

Grid Analysis and Display System (GrADS)(2)

GrADS kasutamine HIROMB GRIB failide jaoks

Win32e GrADS is a port of Brian Doty 's popular Grid Analysis and Display System (GrADS) to the x86 PC running 32-bit MS Windows operating sytems (win9x, winNT, win2000), without the need for installing an X server

GRIB failide lugemiseks peab töökataloogis olema:GRIB andmefail (HIROMB)BS01_200709040000+000H00MHIROMB indeksfail bs01.idxAndmete defineerimisfail bs01.ctl Projektsioonide jaoks skript bsmap.gs

Installeerimine (Win32e GrADS 1.8sl11)1. Käivita “grads-1.8sl11-win32e.exe” (http://ftp.kumamoto-u.ac.jp/pub/.2/graphic/grads/1.8/)

2. Tekita environment variabled (system propertiesadvanced environment variables)

• GADDIR=C:\Program Files\PCGrADS\dat• DISPLAY=800x600x16M

GrADS-i käivitamine cygwin keskkonnas1. Järgi installeerimisjuhendit GrADS tarkvara installeerimisjuhend etc.docx2. Käivita XWin Server3. Mine töökataloogi ja käivita GrADS käsuga ‘grads’

GrADS töötab käsuridadega:projektsioonideks: run bsmap.gsandmed sisse: open bs01.ctl

defineeritakse koordinaadid (üks väärtus või vahemik)kui kaks vahemikku on tulemuseks kaart, kui üks siis graafik

sügavuste vahemik suuremast väärtusest väiksemani

muutuja nimi võetakse bs01.ctl failist

Temperatuur pinnal:

set lev 4d tmp

Soolsus:d salty

Põhikäsud: open failinimi.ctl- avab failiset lev maxsügavus minsügavus- muudab sügavustset lat minlat maxlat- muudab latituutiset lon minlon maxlond muutujanimi- kuvab muutujac- puhastab ekraaniset gxout graafikutüüp- vahetab graafiku tüüpiprintim väljundfaili_nimi.png white x1600 y1200- salvestab ekraanil oleva pildi png faili valge taustagahttp://www.iges.org/grads/gadoc/gadocindex.html

Kõik käsud on võimalik kirjutada skriptifaili nt myscript.gs

Skripti kasutamise plussid ja miinused:

•Kui midagi valesti läheb ei pea jälle otsast alustama•Skript jääb alles ja seda on järgmine kord hea kasutada kui vaja läheb•Kui vaja teha mitu sarnast pilti saab palju kiiremini valmis•Alustades natukene ebamugavam töötada

'set gxout shaded''d dslm''set gxout vector''set arrscl 1 40''set arrowhead 0.015''set ccolor 1''d skip(ugrd,5,10);skip(vgrd,5,10)'

GrADS skriptid* Sample script by Priidik Lagemaa to plot some sample plots for lecture* First clear the display'c'* open control file'open ../dat/bs01.ctl'* set projections'run bsmap.gs'* set x,y,z limits and/or levels'set lev 4''set lon 21 30''set lat 56.5 61'* set output graph type'set gxout shaded'* display variable'd tmp'* draw contours'set gxout contour''d tmp'* draw legend and title'run cbarn''draw title Temperatuur'* save as png image with white background'printim ../dat/tmp.png white x1600 y1200‘*There MUST be at least one empty line at the end of script

Ülesanne 2

Teha gradsi skriptid, mis joonistavad kaardid, lõiked ja graafikud Eesti rannikumeres. Kaardi projektsioonid paika panna ja varustada kontuurjoontega. Kõik joonised varustada legendiga ja pealkirjaga. Salvestada png formaadis valge taustaga.

1) temperatuur TMP2) soolsus SALTY3) veetase DSLM

Kaardi piirid, lõike ja graafiku punkt valida ise. Tulemused ja skriptid saata

priidik.lagemaa@msi.ttu.ee

Ülesanne 3 (valida kas ülesanne 2 või 3)

Teha gradsi skript, mis joonistab põhjakihi soolsuse Eesti rannikumeres. Kaardi projektsioonid paika panna, varustada legendiga ja pealkirjaga. Salvestada png formaadis valge taustaga.

Kaardi piirid valida ise.

Tulemused ja skriptid saata priidik.lagemaa@msi.ttu.ee