Changes between Version 4 and Version 5 of HowTo_nco_netcdf


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Timestamp:
2014-11-21T11:55:07+01:00 (10 years ago)
Author:
zpoussi
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  • HowTo_nco_netcdf

    v4 v5  
    1  
    2 = Manual = 
    3 Please have a look at if you want to make some operations on netcdf files : http://nco.sourceforge.net/#Definition 
    4  
    5 The manual can be downloaded as a pdf : http://nco.sourceforge.net/nco.pdf 
    6  
    7 You may have a look at one of the associated forum if you encounter some problems when using it. 
    8 http://sourceforge.net/projects/nco/forums/forum/9830 
    9  
    10  
    11 == Consulting netcdf files on a dods server == 
    12  
    13 For netcdf files available on an OpenDAP/DODS server, one can see the format by adding .dds at the end of the file. 
    14 Exemple : [[http://dods.ipsl.jussieu.fr/cgi-bin/nph-dods/database/climato/CRU_precipitation.nc.dds]] 
    15  
    16 More explanation on [[http://docs.opendap.org/index.php/QuickStart]] and [[http://www.opendap.org/pub/dods/ps-docs/guide.pdf]] 
    17  
    18  
    19 == Specific notes for the dods in Jussieu == 
    20  
    21 To activate the dods fonctionnality, one should use the URL : [[http://dods.ipsl.jussieu.fr/cgi-bin/nph-dods/]] rather than [[http://dods.ipsl.jussieu.fr/]] 
    22  
    23 For exemple, to see the characteristics of the CRU precipitation file : 
    24 [[http://dods.ipsl.jussieu.fr/cgi-bin/nph-dods/database/climato/CRU_precipitation.nc.dds]] 
    25  
    26 Or to get a subset of it : 
    27 [[http://dods.ipsl.jussieu.fr/cgi-bin/nph-dods/database/climato/CRU_precipitation.nc.html]] 
    28  
    29  
    30 More info on [[http://wiki.ipsl.jussieu.fr/wiki_ipsl/ServeurDODSintro]] 
    31  
    32  
    33 == Example of use == 
    34  
    35  
    36 === commande NetCDF Arithmetic Processor ncap === 
    37  
    38 <code> 
    39    ncap -s "C_tot=VEGET_MAX*(CARBON_PASSIVE+CARBON_ACTIVE+LITTER);C_tot@missing_value=CARBON_PASSIVE@missing_value" soilc_af2002.nc my_soilc_af2002.nc 
    40 </code> 
    41  
    42  
    43 === commande ncrcat === 
    44  
    45 concatenate the variables file_{23..32}.nc changing 2 digits on the number by step of 1 
    46  
    47 <code> 
    48    ncrcat -n 10,2,1 file_23.nc file_global.nc 
    49 </code> 
    50  
    51  
    52 === commande ncwa === 
    53  
    54 Calculate the mean over various dimensions. 
    55  
    56  
    57 === commande ncatted === 
    58  
    59 o, meaning Overwrite (other possible options : a c d m ) a global attribute entitled nbyear which is a double d (other possible options : f d l s c b) 
    60  
    61 <code> 
    62    ncatted -O -a nbyear,global,o,d,$ny stomate_forcing_all.nc 
    63 </code> 
    64  
    65  
    66 Pour modifier rapidement l'année de départ (!attention aux calendriers grégoriens pour lesquels on n'a pas le droit de procéder de la sorte!!!), c'est time_counter:units qui est interprété par ferret et non time_counter:origin. Cf /home/orchidee01/pbrender/ORCHIDEE/MERGE_PP/AGOUFOU_SPINUP_PP/SPINUP_COMPLET_v3/change_date   
    67  
    68 <code> 
    69    #!/bin/bash 
    70    ncrcat -O run_100?/stomate_history.nc MA_Ago_stomate_history.nc  
    71   
    72    n_or=$( ncdump -h MA_Ago_stomate_history.nc |grep time_origin| grep -m 1 -o -E \".*\"|sed "s/2005/$[2005-109]/"|sed 's/"//g')  
    73    n_unit=$( ncdump -h MA_Ago_stomate_history.nc |grep time_counter:units| grep -m 1 -o -E \".*\"|sed "s/2005/$[2005-109]/"|sed 's/"//g')  
    74   
    75    ncatted -O -a time_origin,time_counter,o,c,"${n_or}" MA_Ago_stomate_history.nc  
    76    ncatted -O -a units,time_counter,o,c,"${n_unit}" MA_Ago_stomate_history.nc  
    77 </code> 
    78  
    79  
    80 === Sélection d'une partie d'un fichier netcdf === 
    81  
    82 <code> 
    83    ncks -d tstep,0,17519 wankame_gapfilled.nc wankama_gapfilled_2005.nc 
    84 </code> 
    85  
    86  
    87 === Conversion to ascii and reverse === 
    88  
    89 Pour rapide examen de la structure 
    90  
    91 <code>  
    92    ncdump -c 
    93 </code> 
    94  
    95 Pour l'extraction ascii d'une variable 
    96  
    97 <code> 
    98    ncdump -v temp -f fortran -n name > output.cdl 
    99 </code> 
    100  
    101 Pour récupérer un fichier netcdf à partir de la fraction extraite 
    102  
    103 <code> 
    104    ncgen -b -o my_new_name output.cdl 
    105 </code> 
    106  
    107 Utile aussi quand on rencontre un problème sur une commande par exemple ncatted. Ie pour faire des corrections à la main ! 
    108  
    109  
    110 === ncview === 
    111  
    112 <code> 
    113    ncview 
    114 </code> 
    115  
    116 Installation : 
    117 <code> 
    118    sudo apt-get install xorg-dev netcdfg-dev 
    119    ./configure --x-libraries=/usr/lib 
    120    make 
    121    sudo make install 
    122 </code> 
    123  
    124 Voir aussi cdat et vcdat comme utilitaires de visualisation rapide 
    125  
    126  
    127 === ncap2 === 
    128 <code> 
    129    ncap2 -O -v -s 'gpp_moy=(GPP*VEGET_MAX).avg($PFT)' stomate_history.nc my_history.nc 
    130 </code> 
    131  
    132 Voir exemples de commandes sur : http://nco.sourceforge.net/ncap2.in 
    133  
    134  
    135 === ncpdq === 
    136  
    137 ncpdq makes it possible to concatenate files along any dimension, not just the record dimension. First, use ncpdq to convert the dimension to be concatenated (i.e., extended with data from other files) into the record dimension. As a concrete example, say that files x_01.nc, x_02.nc, ... x_10.nc contain time-evolving datasets from spatially adjacent regions. The time and spatial coordinates are time and x, respectively. Initially the record dimension is time. Our goal is to create a single file that contains joins all the spatially adjacent regions into one single time-evolving dataset. 
    138  
    139 <code> 
    140    for idx in 01 02 03 04 05 06 07 08 09 10; do # Bourne Shell 
    141    ncpdq -a x,time x_${idx}.nc foo_${idx}.nc # Make x record dimension 
    142    done 
    143    ncrcat foo_??.nc out.nc       # Concatenate along x 
    144    ncpdq -a time,x out.nc out.nc # Revert to time as record dimension 
    145 </code> 
    146  
    147