source: lmdz_wrf/trunk/tools/nc_var.py @ 2195

Last change on this file since 2195 was 2195, checked in by lfita, 6 years ago

Adding:

  • `compute_slice2Dstats': Function to compute stats of variables of a file following slices along 2 variables
  • Property svn:executable set to *
File size: 34.9 KB
RevLine 
[192]1#!/usr/bin/python
[1217]2# Python to manage netCDF files.
3# From L. Fita work in different places: CCRC (Australia), LMD (France)
[1219]4# More information at: http://www.xn--llusfb-5va.cat/python/PyNCplot
[1217]5#
6# pyNCplot and its component nc_var.py comes with ABSOLUTELY NO WARRANTY.
7# This work is licendes under a Creative Commons
8#   Attribution-ShareAlike 4.0 International License (http://creativecommons.org/licenses/by-sa/4.0)
9#
10
[1484]11## e.g. # nc_var.py -o lonlat_polygon -f wrfout_d01_1995-01-01_00:00:00 -S star.dat -v XLONG,XLAT
[1494]12## e.g. # nc_var.py -o maskvar -f SouthAm_Climzones_masked.nc -S 'geo_em.d01.nc:LANDMASK:Time|0:0' -v region:lon,lat
[1497]13## e.g. # nc_var.py -o addDim -S 128 -f SouthAm_Climzones.nc -v Lstring
14## e.g. # nc_var.py -o addVar -S 'reg,Lstring|region_name@name!of!the!regions@-|c' -f SouthAm_Climzones.nc -v regionn
15## e.g. # nc_var.py -o varaddattr -f SouthAm_Climzones.nc -S 'grid_mapping_name|Mercator' -v Mercator
16## e.g. # nc_var.py -o varaddattrk -f SouthAm_Climzones.nc -S 'longitude_of_central_meridian|-60.0|R' -v Mercator
17## e.g. # nc_var.py -o setvar_asciivalues -S 'nombres_zonas.dat' -f SouthAm_Climzones.nc -v regionn
[1627]18## e.g. # nc_var.py -o WRF_to_newCF -f wrfout_d01_1995-01-01_00\:00\:00 -S 'XLONG:XLAT:Times:19491201000000:minutes' -v QVAPOR,T2,Q2
[1742]19## e.g. # nc_var.py -o reconstruct_matrix_from_vector -f cruncep_halfdeg_1958.nc -S 'nav_lon:nav_lat:-90.:-7.:-67.:15.:latlon:0.5:0.5:0.05' -v all
[1855]20## e.g. # nc_var.py -o nc_var.py -o CFmorzization -S 'X|west_east|XLONG,Y|south_north|XLAT,T|Time|WRFtime,Z|bottom_top|ZNU:GlobalAttr1995.inf:proj1995.inf' -f ~/PY/wrfout_d01_1995-01-01_00\:00\:00 -v QFX@instantaneous@None
[1857]21## e.g.# nc_var.py -o CFmorzization -S 'X|west_east|XLONG,Y|south_north|XLAT,T|Time|WRFtime,Z|bottom_top|ZNU:GlobalAttr1995.inf:proj1995.inf' -f ~/PY/wrfout_d01_1995-01-01_00\:00\:00 -v 'RAINC@time:!accumulation@WRFtime_bnds|h|3'
[1882]22## e.g. # nc_var.py -o dimrm -S removevar -f wrfout_d01_1995-01-01_00:00:00 -v west_east
23## e.g. # nc_var.py -o ifile -f ../PY/wrfout_d01_1995-01-01_00:00:00
[1884]24## e.g. # nc_var.py -o splitfile_dim -S bottom_top:ZNU:QVAPOR_ZNU:.4f -v QVAPOR,XLONG,XLAT,Times -f ~/PY/wrfout_d01_1995-01-01_00:00:00
[1889]25## e.g. # nc_var.py -o itime -S WRFtime -f ../PY/wrfout_d01_1995-01-01_00:00:00 -v Times
[1939]26## e.g. # nc_var.py -o get_point -S 'XLONG:XLAT:Time|0' -f /home/lluis/PY/wrfout_d01_1995-01-01_00:00:00 -v -45.,-30.
27## e.g. # nc_var.py -o get_time -S '1422759600;seconds!since!1949-12-01!00:00:00' -f /home/lluis/PY/wrfout_d01_1995-01-01_00:00:00 -v WRFtime
[1959]28## e.g. # nc_var.py -o join_singlestation_obsfiles -S 'obs/sfc_CAM:OBSnetcdf' -v all
[2061]29## e.g. # nc_var.py -o join_sounding_obsfiles -S .:UWyoming_snd_1 -v all
[1484]30
[418]31## e.g. ccrc468-17 # ./nc_var.py -v time -f 123/CCRC_NARCliM_Sydney_All_1990-1999_pr10max.nc -o out -S 1:-1
32## e.g. ccrc468-17 # ./nc_var.py -v prac -f xyz/CCRC_NARCliM_Sydney_DAM_1990-1999_prac.nc -o mname -S pluja
33## e.g. ccrc468-17 # ./nc_var.py -v lluis -f CCRC_NARCliM_Sydney_MOM_1990-1999_prac.nc -o addref -S 'prac:standard_name@lluis_variable:long_name@test variable lluis:units@m s-1:0.'
34## e.g. ccrc468-17 # ./nc_var.py -v lluis66 -f ~/UNSW-CCRC-WRF/tools/python/CCRC_NARCliM_Sydney_MOM_1990-1999_prac.nc -o addattr -S 'comment|Lluis Fita-123456'
35## e.g. ccrc468-17 # ./nc_var.py -v lluis66 -f ~/UNSW-CCRC-WRF/tools/python/CCRC_NARCliM_Sydney_MOM_1990-1999_prac.nc -o rmvattr -S 'comment'
36## e.g. acuna # ./nc_var.py -f /d4/lflmd/etudes/WRF_LMDZ/WaquaL/WRF/control/wrfout/wrfout_d01_1979-12-01_00:00:00 -o checkallvars -S 'DateStrLen,Time,soil_layers_stag,bottom_top_stag,bottom_top,west_east_stag,west_east,south_north,south_north_stag:-3,1,2,2,2,-2,-2,-2,-2'
37## e.g. foudre # nc_var.py -f ~/etudes/WRF_LMDZ/tests/wrf_input/AR40.0/wrfout_d01_1979-01-01_00\:00\:00 -o checkallvars -S 'bottom_top_plus1,num_orchidee_soil_levels,lmdz_ksoil_types,DIM0009,DateStrLen,Time,soil_layers_stag,bottom_top_stag,bottom_top,west_east_stag,west_east,south_north,south_north_stag:2,0,0,1,-3,1,2,2,2,-2,-2,-2,-2'
38## e.g. # nc_var.py -o field_stats -f ~/etudes/domains/Polynesie/geo_em.d03.nc -S full -v HGT_M
39## e.g. # nc_var.py -o filter_2dim -S '80,y,x,lon,lat' -f 'tahiti_5m_ll.grd' -v 'z'
40## e.g. # nc_var.py -o selvar -f /home/lluis/PY/met_em.d01.1979-01-01_00:00:00.nc -S 'west_east@XLONG_M,south_north@XLAT_M,num_metgrid_levels@int,Time@Times' -v TT,UU,VV,SKINTEMP
[706]41## e.g. # nc_var.py -o 'Partialmap_Entiremap' -f carteveg5km.nc -S 'longitude,latitude,std,5000.,Goode,Goode_5km.nc' -v vegetation_map
[845]42## e.g. # nc_var.py -o subbasin -f routing.nc -S Caceres,-57.75,-16.25,left
43## e.g. # nc_var.py -o computevar_model -f ~/PY/wrfout_d01_2001-11-11_00:00:00 -S hurs
[847]44## e.g. # nc_var.py -o model_characteristics -f ~/PY/wrfout_d01_2001-11-11_00:00:00 -S WRF
[1005]45## e.g. # nc_var.py -o WRF_toCF -f ~/PY/wrfout_d01_2001-11-11_00:00:00 -S XLONG:XLAT:19491201000000:minutes
[1008]46## e.g. # nc_var.py -o cleaning_varsfile -f ~/PY/wrfout_d01_2001-11-11_00:00:00 -S T2,XLONG,XLAT,Times
[1090]47## e.g. # nc_var.py -o LMDZ_toCF -f LMDZ/AR40/vas_histins_1-1.nc -S 'minutes!since!1949-12-01!00:00:00'
48## e.g. # nc_var.py -o CDO_toCF -f LMDZ/AR40/hfss_reproj-histins.nc
[1050]49## e.g. # nc_var.py -o pinterp -f wrfout_d01_2001-11-11_00\:00\:00 -S 100000.:97500.:95000.:92500.:90000.:85000.:80000.:75000.:70000.:65000.:60000.:55000.:50000.:45000.:40000.:35000.:30000.:25000.:20000.:15000.:10000.:5000.:2500.:1000.:500.:250.,1,0 -v WRFt,WRFrh
[1053]50## e.g. # nc_var.py -o pinterp -f /media/ExtDiskC_ext4/DATA/etudes/WRF_LMDZ/WaquaL_highres/short_copies/LMDZ/AR40/histins_19790101000000-19790304000000_short.nc -S 100000.:97500.:95000.:92500.:90000.:85000.:80000.:75000.:70000.:65000.:60000.:55000.:50000.:45000.:40000.:35000.:30000.:25000.:20000.:15000.:10000.:5000.:2500.:1000.:500.:250.,1,0 -v temp,ovap
[1179]51## e.g. # nc_var.py -o reproject -f analysis/LMDZ/AR40/hurs_histins.nc -S 'lon,lat,analysis/WRF/current/hurs_wrfout.nc,lon,lat,npp,time@time' -v hurs
[1181]52## e.g. # nc_var.py -o field_stats_dim -f /home/lluis/PY/wrfout_d01_2001-11-11_00:00:00 -S 'full,None,None,west_east,XLONG,False' -v 'T2'
[1233]53## e.g. # nc_var.py -o compute_opersvarsfiles -S 'west_east|XLONG|-1;south_north|XLAT|-1;Time|Times|3@add|wrfout_d01_2001-11-11_00:00:00|T2%west_east|XLONG|-1;south_north|XLAT|-1;Time|Times|3@subc,273.15|wrfout_d01_2001-11-11_00:00:00|None' -v 'tempC,air!temperature,C'
[1237]54## e.g. # nc_var.py -o compute_opersvarsfiles -S 'lon|lon|-1;lat|lat|-1;time_counter|time_counter|-1@forwrdderiv,1,1,2|/ccc/store/cont003/gen7593/fitaborl/etudes/DynamicoESM/aquaplanet/AR40/19800101000000-19810101000000/histday.nc|t2m' -v 'tasderiv,x-derivative|of|air|temperature,K
[1360]55## e.g. # nc_var.py -o getvars_tofile -S soils_param_Zobler_textXIOS.nc -f soils_param_colorXIOS.nc -v 'soiltext,soiltexttypes'
[1375]56## e.g. # nc_var.py -o addVar -S 'lon,lat|mask@mask@1|f' -f new_ORCHIDEE_13PFTmap_2010_cmpi6_LUH2v2h.nc -v mask
57## e.g. # nc_var.py -o setvar_nc -S 'new_ORCHIDEE_13PFTmap_2010_cmpi6_LUH2v2h.nc,maxvegetfrac,veget;0' -f new_ORCHIDEE_13PFTmap_2010_cmpi6_LUH2v2h.nc -v mask
58## e.g. $ nc_var.py -o VarVal_FillValue -S '0.,eq,std' -f new_lai2D.nc -v LAI
59## e.g. # nc_var.py -o rm_FillValue -f new_ORCHIDEE_13PFTmap_2010_cmpi6_LUH2v2h.nc -S 0 -v mask
[1406]60## e.g. # nc_var.py -o curve_section -f /home/lluis/PY/test.nc -S 'gridline,x,y,8.,8.,16.,16.,32' -v all
[1597]61## e.g. # nc_var.py -o merge_files -S 'plev|plev,time|time:merged.nc' -f 'ncobs/AliceSprings/snd_94326_198201-198201.nc,ncobs/AliceSprings/snd_94326_198202-198202.nc' -v 'plev,time'
[2165]62## e.g. # nc_var.py -o temporal_stats -S 'Time:WRFtime:day@1@min,LTday@-3@1@min:bottom_top@ZNU,south_north@XLAT,west_east@XLONG' -f wrfout_d01_1995-01-01_00:00:00 -v T2,Q2
[2168]63## e.g. # nc_var.py -o retrieve_stations -f wrfout_d01_1995-01-01_00:00:00 -S 'tmin_percentiles.nc:stname:None:stlon:stlat:None:nearest:west_east:XLONG:south_north:XLAT:HGT:Time:WRFtime' -v T2,QVAPOR
[2195]64## e.g. # nc_var.py -o compute_slice2Dstats -S 'XLAT,-63.,19.,2.,HGT,250.,7000.,500.,Time|Times:west_east|XLONG:south_north|XLAT' -f wrfout_d01_1995-01-01_00:00:00 -v T2,Q2
[192]65
66from optparse import OptionParser
67import numpy as np
68from netCDF4 import Dataset as NetCDFFile
69import os
70import re
71import nc_var_tools as ncvar
[759]72# Using 'generic_tools.py'
[748]73import generic_tools as gen
[192]74
[1490]75# addDim: Operation to add a new dimension in a file
[1375]76# addVar: Operation to add a new variable in a file using exisintg dimensions
[1215]77# addvals: Function to add values to a given variable at a given dimension
78# CDO_toCF: Function to pass a CDO output file to CF-conventions
[1845]79# CFmorzization: Function to provide a CF-compilation version of a variable within a file
[1215]80# chdimname: Changing the name of the dimension
81# changevartype: Function to change the type of a variable (when possible)
82# checkallvars: Function to check all variables of a file
83# checkAllValues: Function to check for variables with along all their dimensions with the same value in a file
84# checkNaNs: Function to check for NaN values over all variables in a file
85# chgtimestep: Function to change the values of a given time-step of a variable inside a netCDF for values from a nother file
86# chvarname: Changing the name of the variable
87# cleaning_varsfile: Function to keep a list of varibales from a file
88# compute_deaccum: Function to compute deaccum: deaccumulation of a variable (VAR[t+1]-VAR[t])
89# compute_opersvarsfiles: Function to compute opersvarfiles: operation of variables from different files
90# compute_opervaralltime: Function to compute opervaralltime: operation of variable successible allover the time-steps
91# compute_opervartimes: Function to compute opervartimes: operation of variable for a given sub-set of time-steps
[2195]92# compute_slice2Dstats: Function to compute stats of variables of a file following slices along 2 variables
[1215]93# compute_tevolboxtraj: Function to compute tevolboxtraj: temporal evolution at a given point along a box following a trajectory
94# computevar_model: Function to provide the way to compute a CF-variable providing its name
[1406]95# curve_section: Function to provide a section of a file following a given curve
[1215]96# DatesFiles: Function to find different time values on a series of WRF files in a folder
97# DataSetSection: Function to get a section (values along a dimension) of a given data-set
98# DataSetSection_multidims: Function to get a section (values along multiple dimensions) of a given data-set
99# DataSetSection_multivars: Function to get a section (values along multiple variables) of a given data-set
[1295]100# DYNAMICO_toCF: Function to pass a DYNAMICO original file to CF-conventions
[1879]101# dimrm: Removing a dimension from a file
[1215]102# dimToUnlimited: Operation to create an unlimited dimension from an existing one
103# dimVar_creation: Function to add a 1D variable with the size of a given dimension in a file
104# fattradd: Adding attributes from a reference file
105# fdimadd: Adding dimension from another reference file
106# fgaddattr: Adding global attributes from a reference file
107# field_stats: Function to retrieve statistics from a field
108# field_stats_dim: Function to retrieve statistics from a field along dimensions
109# file_creation: Operation to create a file with one variable with a given set of dimensions
110# file_oper_alongdims: Function to operate a file along different dimensions of a variable
111# filter_2dim: Function to filter along 2 dimensions (moving grid-box means of a given size) values of the netCDF file
112# flipdim: flips the value following one dimension
113# fvaradd: Adding variable (and all its attributes and dimensions) from a reference file to a file
114# gaddattrk: Add a global attribute to a netCDF caring about the type. Removes previous attribute if it exist
115# gaddattr: Add a global attribute to a netCDF. Removes previous attribute if it exist
116# get_attribute: Function to get an attribute from a netCDF file
[1939]117# get_point: Function to provide the closest grid point to a given lat,lon
118# get_time: Function to provide the closest time-step to a given time
[1215]119# get_namelist_vars: Function to get namelist-like  values ([varname] = [value])
120# get_Variables: Function to get a list of variables from an existing file
121# getvalues_lonlat: Function to retrieve the values from the closest grid point to a set of longitude, latitude values
[1360]122# getvars_tofile: Function to get variables from a file and pass them to another one
[1215]123# grattr: Function to read a global atribute
124# grmattr: Removing a global attribute
125# idims: Give all the dimensions names of a file
[1881]126# ifile: Function to provide some information from a given file
[1215]127# igattrs: Give all the global attributes of a file
128# increaseDimvar: Function to increase with 1 dimension an existing variable within a netcdf file. Values of
129#   the variable will be repeated along the new dimension
130# isgattrs: Give a single global attribute of a file and its type
131# isvattrs: Give a single attribute of a variable
[1889]132# itime: Function to provide information of the time from a netCDF file
[1215]133# ivars: Give all the variable names of a file
134# ivattrs: Give all the attributes of a variable and its type
[2061]135# join_singlestation_obsfiles: Function to join files from 'single-station'
136#   `create_OBSnetcdf.py' script to create a single file
137# join_sounding_obsfiles: Function to join 1D variables from files generated by
138#   `UWyoming_snd_nc.py' script to create a single file
[1215]139# LMDZ_toCF: Function to pass a LMDZ original file to CF-conventions
[1484]140# lonlat_polygon: Function to define a lon/lat region giving the coordinates of the vertexs of a given polygon
[1494]141# maskvar: Function to mask a variable using another variable to mask it. Only need to share at least 1 dimension with the same size (no need same name)
[1597]142# merge_files: Function to merge variables from two files
[1215]143# model_characteristics: Function to provide major characterisitcs of a given model output
[1428]144# mthDYNAMICO_toCF: Function to pass a mthDYNAMICO original file to CF-conventions
[1215]145# ncreplace: Function to replace something from a netCDF file
146# ncstepdiff: Function to compute differencies between time-steps (deacumulate) a netCDF file
147# netcdf_concatenation: Function to concatenate netCDF files for a given set of variables
148# netcdf_fold_concatenation: Function to concatenate netCDF files in a given folder for a given set of variables
149# netcdf_fold_concatenation_HMT: Function to concatenate netCDF files in a given folder for a given set of variables
150#   giving Header, Middle, Tail for the name files
[1732]151# reconstruct_matrix_from_vector: Function to reconstruct a 2D matrix from a pair of syncronized vectors with the positions on x and y coordinates
[1215]152# reproject: Function to reproject values to another one
[1375]153# rm_FillValue: Operation to remove the _FillValue from a variable inside a netCDF file
[1215]154# Partialmap_Entiremap: Function to transform from a partial global map (e.g.: only land points) to an entire one
155#   Coincidence of points is done throughout a first guess from fractions of the total domain of search
156# Partialmap_EntiremapFor: Function to transform from a partial global map (e.g.: only land points) to an entire one
157#   using Fortran code Coincidence of points is done throughout a first guess from fractions of the total domain of search
158# Partialmap_EntiremapForExact: Function to transform from a partial global map (e.g.: only land points) to an entire
159#   one using Fortran code with exact location Coincidence of points is done throughout a first guess from fractions of
160#   the total domain of search
161# pinterp: Function to vertically interpolate using subroutines from the p_interp.F90 NCAR program
162# remapnn: Function to remap to the nearest neightbor a variable using projection from another file
[2168]163# retrieve_stations: Function to retrieve temporal values at given stations provided by a secondary netcdf
[1215]164# seasmean: Function to compute the seasonal mean of a variable
165# sellonlatbox: Function to select a lotlan box from a data-set
166# sellonlatlevbox: Function to select a lotlan box and a given level from a data-set
167# selvar: Function to select a series of variables from a netcdf file. Variables with
[1375]168# setvar_asciivalues: Function to set de values of a variable with an ASCII file (common Fortran-like format)
169# setvar_nc: Operation to set values of a variable from values of an other one
[1215]170# sorttimesmat: Function to sort the time values of a given file
171# spacemean: Function to retrieve a space mean series from a multidimensional variable of a file
172# SpatialWeightedMean: Function to compute the spatial mean using weights from a netCDF file
[1883]173# splitfile_dim: Function to split a file along a given dimension with a new file for each different value along the dimension (assuming resultant vardim of rank-1)
[1215]174# statcompare_files: Python script to statistically compare two different files
175# subbasin: Function to retrieve the subbasin (all the sub-flows untila a given lon,lat)
176# submns: Function to retrieve a series of months from a file
177# subyrs: Function to retrieve a series of years from a file
[2165]178# temporal_stats: Function to compute temporal statistics. Rank of the variables are
179#   preserved along other non-temporal dimensions
[1215]180# TimeInf: Function to print all the information from the variable time
181# time_reset: Function to re-set the time axis of a file
182# TimeSplitmat: Function to transform a file with CFtimes to a matrix [Nyear,Nmonth,Nday,Nhour,Nminute,Nsecond]
183# timemean: Function to retrieve a time mean series from a multidimensional variable of a file
184# valmod: Function to modify the value of a variable
185# valmod_dim: Function to modify the value of a variable at a given dimension and value
186# varaddattrk: Add an attribute to a variable caring about the type
187# varaddattr: Add an attribute to a variable. Removes previous attribute if it exists
188# varaddref: Function to add a variable in an existing file copying characteristics from an existing one
189# var_creation: Operation to create a new variable in a file with a given set of dimensions
190# varout: Function when we want to output variable values
191# varrmattr: Removing an attribute from a variable
192# varrm: Removing a variable from a file
193# VarVal_FillValue: Function to transform a given value from a given variable to _FillValue in a netCDF file
194# vrattr: Function to remove an atribute from a variable
195# WRF_d0Nref: Function for the generation of an extra WRF domain from a given one
196# WRF_CFlonlat_creation: Function to add a CF-convention longitude/latitude variables in a WRF file
197# WRF_CFtime_creation: Function to add a CF-convention time unit in a WRF file
198# WRF_CFxtime_creation: Function to add a CF-convention time unit in a WRF file using variable 'XTIME'
199# WRF_toCF: Function to pass a WRF original file to CF-conventions
[1627]200# WRF_to_newCF: Function to pass a WRF original file to new CF-conventions file
[1215]201
[1845]202operations=['addDim', 'addVar', 'addvals', 'CDO_toCF', 'CFmorzization',              \
203  'chdimname', 'changevartype',                                                      \
[1375]204  'checkallvars', 'checkAllValues', 'checkNaNs',                                     \
[1008]205  'chgtimestep', 'chvarname', 'cleaning_varsfile', 'compute_deaccum',                \
206  'compute_opersvarsfiles',                                                          \
[2195]207  'compute_opervaralltime', 'compute_opervartimes', 'compute_slice2Dstats',          \
208  'compute_tevolboxtraj',                                                            \
[1406]209  'computevar_model', 'curve_section', 'DatesFiles',                                 \
[576]210  'DataSetSection', 'DataSetSection_multidims', 'DataSetSection_multivars',          \
[1879]211  'DYNAMICO_toCF', 'dimrm', 'dimToUnlimited', 'dimVar_creation',                     \
[576]212  'fattradd',                                                                        \
[1181]213  'fdimadd', 'fgaddattr', 'field_stats', 'field_stats_dim', 'file_creation',         \
214  'file_oper_alongdims', 'filter_2dim',                                              \
[656]215  'flipdim', 'fvaradd', 'gaddattrk', 'gaddattr', 'get_attribute',                    \
[1939]216  'get_point', 'get_time', 'get_namelist_vars', 'get_Variables',                     \
[1360]217  'getvalues_lonlat', 'getvars_tofile', 'grattr',                                    \
[1881]218  'grmattr', 'idims', 'ifile', 'igattrs', 'increaseDimvar', 'isgattrs',              \
[1959]219  'isvattrs', 'itime', 'ivars', 'ivattrs', 'join_singlestation_obsfiles',            \
[2061]220  'join_sounding_obsfiles', 'LMDZ_toCF', 'lonlat_polygon', 'maskvar',                \
[1597]221  'merge_files', 'model_characteristics',                                            \
[1428]222  'mthDYNAMICO_toCF', 'ncreplace', 'ncstepdiff', 'netcdf_concatenation',             \
223  'netcdf_fold_concatenation',                                                       \
[1173]224  'netcdf_fold_concatenation_HMT', 'reproject', 'Partialmap_Entiremap',              \
[905]225  'Partialmap_EntiremapFor', 'Partialmap_EntiremapForExact',                         \
[2168]226  'pinterp', 'reconstruct_matrix_from_vector', 'remapnn', 'retrieve_stations',       \
227  'rm_FillValue',                                                                    \
[418]228  'seasmean', 'sellonlatbox', 'sellonlatlevbox', 'selvar', 'setvar_asciivalues',     \
[1375]229  'setvar_nc', 'sorttimesmat', 'spacemean', 'SpatialWeightedMean',                   \
[1883]230  'splitfile_dim', 'statcompare_files',                                              \
[2165]231  'subbasin', 'submns', 'subyrs', 'temporal_stats', 'TimeInf', 'time_reset',         \
[533]232  'TimeSplitmat', 'timemean', 'valmod', 'valmod_dim','varaddattrk', 'varaddattr',    \
233  'varaddref',                                                                       \
[666]234  'var_creation', 'varout', 'varoutold', 'varrmattr', 'varrm', 'VarVal_FillValue',   \
235  'vrattr', 'WRF_d0Nref',                                                            \
[192]236  'WRF_CFlonlat_creation', 'WRF_CFtime_creation', 'WRF_CFxtime_creation',            \
[1627]237  'list_operations', 'WRF_toCF', 'WRF_to_newCF']
[192]238
239### Options
240##string_operation="operation to make: " + '\n' + " out, output values -S inidim1,[inidim2,...]:enddim1,[enddim2,...]"
241string_operation="""operation to make:
242  addgattr, add a new global attribute: addatr -S [attrname]|[attrvalue]
243  addvattr, add a new attribute to any given variable: addatr -S [attrname]|[attrvalue]
244  addref, add a new variable with dimension and attributes from an already existing 'variable ref' in the file and -S [variable ref]:[attr name]@[value]:[[attr2]@[value2], ...]:[value/file with values]  mname, modify name -S newname
245  checkallvalrs: Function to check all variables of a file: -S [dimn1],[[dimn2],...,[dimnN]]:[dim1],[[dim2],...,[dimN]]
246  mname, modify name -S newname
247  out, output values -S inidim1,[inidim2,...]:enddim1,[enddim2,...]
248  valmod, modifiy values of variable -S [modification]:
249     sumc,[constant]: add [constant] to variables values
250     subc,[constant]: substract [constant] to variables values
251     mulc,[constant]: multipy by [constant] to variables values
252     divc,[constant]: divide by [constant] to variables values
253  rmgattr, remove a global attribute: rmgattr -S [attrname]
254  rmvattr, remove an attribute to any given variable: rmvattr -S [attrname]
255"""
256
257#print string_operation
258
[748]259operationnames = "'" + gen.numVector_String(operations, "', '") + "'"
[192]260
261parser = OptionParser()
[820]262parser.add_option("-f", "--netCDF_file", dest="ncfile", help="file to use", 
263  metavar="FILE")
[192]264parser.add_option("-o", "--operation", type='choice', dest="operation", 
265  choices=operations, help="operation to make: " + operationnames, metavar="OPER")
[820]266parser.add_option("-S", "--valueS", dest="values", 
267  help="values to use according to the operation (when applicable); '-h' specific help of the operation", metavar="VALUES")
[192]268parser.add_option("-v", "--variable", dest="varname",
[820]269  help="variable to use (when applicable)", metavar="VAR")
[192]270
271(opts, args) = parser.parse_args()
272
273#if opts.help:
274#  parser.print_help()
275#  print string_operation
276#  sys.exit()
277
278#######    #######
279## MAIN
280    #######
281
282# Operations which file name is not a real file
[1311]283NotCheckingFile = ['DatesFiles', 'compute_opersvarsfiles', 'file_creation',          \
[2061]284  'join_singlestation_obsfiles', 'join_sounding_obsfiles', 'list_operations',        \
285  'merge_files',                                                                     \
[905]286  'model_characteristics', 'netcdf_concatenation', 'netcdf_fold_concatenation',      \
287  'netcdf_fold_concatenation_HMT']
[192]288
289####### ###### ##### #### ### ## #
290errormsg='ERROR -- error -- ERROR -- error'
291
292varn=opts.varname
293oper=opts.operation
294
[1271]295if opts.operation is None:
296    print errormsg
297    print '  No operation provided !!'
298    print "  an operation must be provided as '-o [operationname]' "
299    quit(-1)
300
[192]301if opts.ncfile is not None and not os.path.isfile(opts.ncfile) and                   \
[1978]302  not gen.searchInlist(NotCheckingFile,oper) and opts.ncfile != 'h':
[192]303    print errormsg
[1978]304    print "  File '" + opts.ncfile + "' does not exist !!"
[192]305    quit(-1)
[1275]306elif opts.ncfile is None and not gen.searchInlist(NotCheckingFile,oper) and          \
307  opts.values != 'h':
[1271]308    print errormsg
309    print '  No file provided !!'
310    print "  a file must be provided as '-f [filename]' "
311    quit(-1)
[192]312
[1490]313if oper == 'addDim':
314    ncvar.addDim(opts.values, opts.ncfile, opts.varname)
315elif oper == 'addVar':
[1375]316    ncvar.addVar(opts.values, opts.ncfile, opts.varname)
317elif oper == 'addvals':
[192]318    ncvar.addvals(opts.values, opts.ncfile, opts.varname)
[1062]319elif oper == 'CDO_toCF':
320    ncvar.CDO_toCF(opts.ncfile)
[1845]321elif oper == 'CFmorzization':
322    ncvar.CFmorzization(opts.values, opts.ncfile, opts.varname)
[192]323elif oper == 'chdimname':
[870]324    ncvar.chdimname(opts.values, opts.ncfile)
[408]325elif oper == 'changevartype':
326    ncvar.changevartype(opts.values, opts.ncfile, opts.varname)
[192]327elif oper == 'checkallvars':
328    ncvar.checkallvars(opts.values, opts.ncfile)
329elif oper == 'checkAllValues':
330    ncvar.checkAllValues(opts.values, opts.ncfile)
331elif oper == 'checkNaNs':
332    ncvar.checkNaNs(opts.values, opts.ncfile)
333elif oper == 'chgtimestep':
334    ncvar.chgtimestep(opts.values, opts.ncfile, opts.varname)
335elif oper == 'chvarname':
336    ncvar.chvarname(opts.values, opts.ncfile, opts.varname)
[1008]337elif oper == 'cleaning_varsfile':
338    ncvar.cleaning_varsfile(opts.values, opts.ncfile)
[192]339elif oper == 'compute_deaccum':
340    ncvar.compute_deaccum(opts.values, opts.ncfile, opts.varname)
341elif oper == 'compute_opersvarsfiles':
342    ncvar.compute_opersvarsfiles(opts.values, opts.varname)
343elif oper == 'compute_opervaralltime':
344    ncvar.compute_opervaralltime(opts.values, opts.ncfile, opts.varname)
345elif oper == 'compute_opervartimes':
346    ncvar.compute_opervartimes(opts.values, opts.ncfile, opts.varname)
[2195]347elif oper == 'compute_slice2Dstats':
348    ncvar.compute_slice2Dstats(opts.values, opts.ncfile, opts.varname)
[192]349elif oper == 'compute_tevolboxtraj':
350    ncvar.compute_tevolboxtraj(opts.values, opts.ncfile, opts.varname)
[845]351elif oper == 'computevar_model':
352    ncvar.computevar_model(opts.values, opts.ncfile)
[1406]353elif oper == 'curve_section':
354    ncvar.curve_section(opts.values, opts.ncfile, opts.varname)
[192]355elif oper == 'DataSetSection':
356    ncvar.DataSetSection(opts.values, opts.ncfile)
357elif oper == 'DataSetSection_multidims':
[674]358    ncvar.DataSetSection_multidims(opts.values, opts.ncfile, opts.varname)
[576]359elif oper == 'DataSetSection_multivars':
360    ncvar.DataSetSection_multivars(opts.values, opts.ncfile, opts.varname)
[507]361elif oper == 'DatesFiles':
362    ncvar.DatesFiles(opts.values, opts.ncfile, opts.varname)
[1295]363elif oper == 'DYNAMICO_toCF':
364    ncvar.DYNAMICO_toCF(opts.values, opts.ncfile)
[1879]365elif oper == 'dimrm':
366    ncvar.dimrm(opts.ncfile, opts.values, opts.varname)
[397]367elif oper == 'dimToUnlimited':
368    ncvar.dimToUnlimited(opts.values, opts.ncfile)
[192]369elif oper == 'dimVar_creation':
370    ncvar.dimVar_creation(opts.values, opts.ncfile)
371elif oper == 'fattradd':
372    ncvar.fattradd(var, opts.values, opts.ncfile)
373elif oper == 'fdimadd':
374    ncvar.fdimadd(opts.values, opts.ncfile)
375elif oper == 'fgaddattr':
376    ncvar.fgaddattr(opts.values, opts.ncfile)
[386]377elif oper == 'file_creation':
378    ncvar.file_creation(opts.values, opts.ncfile, opts.varname)
[192]379elif oper == 'file_oper_alongdims':
380    ncvar.file_oper_alongdims(opts.values, opts.ncfile, opts.varname)
381elif oper == 'field_stats':
382    ncvar.field_stats(opts.values, opts.ncfile, opts.varname)
[1181]383elif oper == 'field_stats_dim':
384    ncvar.field_stats_dim(opts.values, opts.ncfile, opts.varname)
[192]385elif oper == 'filter_2dim':
386    ncvar.filter_2dim(opts.values, opts.ncfile, opts.varname)
387elif oper == 'flipdim':
388    ncvar.flipdim(opts.values, opts.ncfile, opts.varname)
389elif oper == 'fvaradd':
390    ncvar.fvaradd(opts.values, opts.ncfile)
391elif oper == 'gaddattrk':
392    ncvar.gaddattrk(opts.values, opts.ncfile)
393elif oper == 'gaddattr':
394    ncvar.gaddattr(opts.values, opts.ncfile)
[656]395elif oper == 'get_attribute':
396    ncvar.get_attribute(opts.values, opts.ncfile, opts.varname)
[192]397elif oper == 'get_namelist_vars':
[778]398    ncvar.get_namelist_vars(opts.values, opts.ncfile)
[1939]399elif oper == 'get_point':
400    ncvar.get_point(opts.values, opts.ncfile, opts.varname)
401elif oper == 'get_time':
402    ncvar.get_time(opts.values, opts.ncfile, opts.varname)
[965]403elif oper == 'get_Variables':
[967]404    ncvar.get_Variables(opts.values, opts.ncfile, opts.varname)
[632]405elif oper == 'getvalues_lonlat':
406    ncvar.getvalues_lonlat(opts.values, opts.ncfile)
[1360]407elif oper == 'getvars_tofile':
408    ncvar.getvars_tofile(opts.values, opts.ncfile, opts.varname)
[192]409elif oper == 'grattr':
410    ncvar.grattr(opts.values, opts.ncfile)
411elif oper == 'grmattr':
412    ncvar.grmattr(opts.values, opts.ncfile)
[870]413elif oper == 'idims':
414    ncvar.idims(opts.ncfile)
[1881]415elif oper == 'ifile':
416    ncvar.ifile(opts.ncfile)
[192]417elif oper == 'igattrs':
418    ncvar.igattrs(opts.ncfile)
[404]419elif oper == 'increaseDimvar':
420    ncvar.increaseDimvar(opts.values, opts.ncfile, opts.varname)
[192]421elif oper == 'isgattrs':
422    ncvar.isgattrs(opts.values, opts.ncfile)
423elif oper == 'isvattrs':
424    ncvar.isvattrs(opts.values, opts.ncfile, opts.varname)
[1889]425elif oper == 'itime':
426    ncvar.itime(opts.values, opts.ncfile, opts.varname)
[192]427elif oper == 'ivars':
428    ncvar.ivars(opts.ncfile)
429elif oper == 'ivattrs':
430    ncvar.ivattrs(opts.ncfile, opts.varname)
[1959]431elif oper == 'join_singlestation_obsfiles':
432    ncvar.join_singlestation_obsfiles(opts.values, opts.varname)
[2061]433elif oper == 'join_sounding_obsfiles':
434    ncvar.join_sounding_obsfiles(opts.values, opts.varname)
[192]435elif oper == 'list_operations':
436# From: http://www.diveintopython.net/power_of_introspection/all_together.html
437    object = ncvar
438    for opern in operations:
439        if  opern != 'list_operations': 
440            print opern + '_______ ______ _____ ____ ___ __ _'
441            print getattr(object, opern).__doc__
[1046]442elif oper == 'LMDZ_toCF':
[1090]443    ncvar.LMDZ_toCF(opts.values, opts.ncfile)
[1484]444elif oper == 'lonlat_polygon':
445    ncvar.lonlat_polygon(opts.values, opts.ncfile, opts.varname)
[192]446elif oper == 'maskvar':
447    ncvar.maskvar(opts.values, opts.ncfile, opts.varname)
[1597]448elif oper == 'merge_files':
449    ncvar.merge_files(opts.values, opts.ncfile, opts.varname)
[847]450elif oper == 'model_characteristics':
451    ncvar.model_characteristics(opts.values, opts.ncfile)
[1428]452elif oper == 'mthDYNAMICO_toCF':
453    ncvar.mthDYNAMICO_toCF(opts.values, opts.ncfile)
[192]454elif oper == 'ncreplace':
455    ncvar.ncreplace(opts.values, opts.ncfile, opts.varname)
[311]456elif oper == 'ncstepdiff':
457    ncvar.ncstepdiff(opts.values, opts.ncfile, opts.varname)
[192]458elif oper == 'netcdf_concatenation':
459    ncvar.netcdf_concatenation(opts.ncfile)
460elif oper == 'netcdf_fold_concatenation':
461    ncvar.netcdf_fold_concatenation(opts.values, opts.ncfile, opts.varname)
[905]462elif oper == 'netcdf_fold_concatenation_HMT':
463    ncvar.netcdf_fold_concatenation_HMT(opts.values, opts.ncfile, opts.varname)
[192]464elif oper == 'opersvarsfiles':
465    ncvar.compute_opersvarsfiles(opts.values, opts.varname)
[900]466elif oper == 'pinterp':
467    ncvar.pinterp(opts.values, opts.ncfile, opts.varname)
[409]468elif oper == 'remapnn':
469    ncvar.remapnn(opts.values, opts.ncfile, opts.varname)
[693]470elif oper == 'Partialmap_Entiremap':
471    ncvar.Partialmap_Entiremap(opts.values, opts.ncfile, opts.varname)
[716]472elif oper == 'Partialmap_EntiremapFor':
473    ncvar.Partialmap_EntiremapFor(opts.values, opts.ncfile, opts.varname)
[735]474elif oper == 'Partialmap_EntiremapForExact':
475    ncvar.Partialmap_EntiremapForExact(opts.values, opts.ncfile, opts.varname)
[1732]476elif oper == 'reconstruct_matrix_from_vector':
[1733]477    ncvar.reconstruct_matrix_from_vector(opts.values, opts.ncfile, opts.varname)
[1173]478elif oper == 'reproject':
479    ncvar.reproject(opts.values, opts.ncfile, opts.varname)
[2168]480elif oper == 'retrieve_stations':
481    ncvar.retrieve_stations(opts.values, opts.ncfile, opts.varname)
[1375]482elif oper == 'rm_FillValue':
483    ncvar.rm_FillValue(opts.values, opts.ncfile, opts.varname)
[192]484elif oper == 'seasmean':
485    ncvar.seasmean(timename, opts.ncfile, opts.varname)
486elif oper == 'sellonlatbox':
487    ncvar.sellonlatbox(opts.values, opts.ncfile, opts.varname)
488elif oper == 'sellonlatlevbox':
489    ncvar.sellonlatlevbox(opts.values, opts.ncfile, opts.varname)
[418]490elif oper == 'selvar':
491    ncvar.selvar(opts.values, opts.ncfile, opts.varname)
[192]492elif oper == 'setvar_asciivalues':
493    ncvar.setvar_asciivalues(opts.values, opts.ncfile, opts.varname)
[1375]494elif oper == 'setvar_nc':
495    ncvar.setvar_nc(opts.values, opts.ncfile, opts.varname)
[192]496elif oper == 'sorttimesmat':
497    ncvar.sorttimesmat(opts.ncfile, opts.varname)
498elif oper == 'spacemean':
499    ncvar.spacemean(opts.ncfile, opts.varname)
[662]500elif oper == 'SpatialWeightedMean':
501    ncvar.SpatialWeightedMean(opts.values, opts.ncfile, opts.varname)
[1883]502elif oper == 'splitfile_dim':
503    ncvar.splitfile_dim(opts.values, opts.ncfile, opts.varname)
[192]504elif oper == 'statcompare_files':
505    ncvar.statcompare_files(opts.values)
[815]506elif oper == 'subbasin':
507    ncvar.subbasin(opts.values, opts.ncfile)
[192]508elif oper == 'submns':
509    ncvar.submns(opts.values, opts.ncfile, opts.varname)
510elif oper == 'subyrs':
511    ncvar.subyrs(opts.values, opts.ncfile, opts.varname)
[2165]512elif oper == 'temporal_stats':
513    ncvar.temporal_stats(opts.values, opts.ncfile, opts.varname)
[192]514elif oper == 'TimeInf':
515    ncvar.TimeInf(opts.ncfile, opts.varname)
[1092]516elif oper == 'time_reset':
517    ncvar.time_reset(opts.values, opts.ncfile, opts.varname)
[533]518elif oper == 'TimeSplitmat':
519    ncvar.TimeSplitmat(opts.values, opts.ncfile, opts.varname)
[192]520elif oper == 'timemean':
521    ncvar.timemean(opts.values, opts.ncfile, opts.varname)
522elif oper == 'valmod':
523    ncvar.valmod(opts.values, opts.ncfile, opts.varname)
524elif oper == 'valmod_dim':
525    ncvar.valmod_dim(opts.values, opts.ncfile, opts.varname)
526elif oper == 'varaddattrk':
527    ncvar.varaddattrk(opts.values, opts.ncfile, opts.varname)
528elif oper == 'varaddattr':
529    ncvar.varaddattr(opts.values, opts.ncfile, opts.varname)
530elif oper == 'varaddref':
531    ncvar.varaddref(opts.values, opts.ncfile, opts.varname)
[387]532elif oper == 'var_creation':
533    ncvar.var_creation(opts.values, opts.ncfile, opts.varname)
[192]534elif oper == 'varout':
535    ncvar.varout(opts.values, opts.ncfile, opts.varname)
536elif oper == 'varoutold':
537    ncvar.varoutold(opts.values, opts.ncfile, opts.varname)
538elif oper == 'varrmattr':
539    ncvar.varrmattr(opts.values, opts.ncfile, opts.varname)
540elif oper == 'varrm':
541    ncvar.varrm(opts.ncfile, opts.varname)
[666]542elif oper == 'VarVal_FillValue':
543    ncvar.VarVal_FillValue(opts.values, opts.ncfile, opts.varname)
[192]544elif oper == 'vrattr':
545    ncvar.vrattr(opts.values, opts.ncfile, opts.varname)
546elif oper == 'WRF_d0Nref':
547    ncvar.WRF_d0Nref(opts.values, opts.ncfile)
548elif oper == 'WRF_CFlonlat_creation':
549    ncvar.WRF_CFlonlat_creation(opts.values, opts.ncfile, opts.varname)
550elif oper == 'WRF_CFtime_creation':
551    ncvar.WRF_CFtime_creation(opts.values, opts.ncfile, opts.varname)
552elif oper == 'WRF_CFxtime_creation':
553    ncvar.WRF_CFxtime_creation(opts.values, opts.ncfile, opts.varname)
[1005]554elif oper == 'WRF_toCF':
555    ncvar.WRF_toCF(opts.values, opts.ncfile)
[1627]556elif oper == 'WRF_to_newCF':
557    ncvar.WRF_to_newCF(opts.values, opts.ncfile, opts.varname)
[192]558else:
559    print errormsg
560    print '   The operation ' + oper + ' is not ready !!'
561    print errormsg
562    quit()
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