source: lmdz_wrf/trunk/tools/nc_var.py @ 2453

Last change on this file since 2453 was 2404, checked in by lfita, 6 years ago

Fixing `temporal_stats' by fixing the 'aggday', 'agghour'
  • Property svn:executable set to *
File size: 40.1 KB
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1#!/usr/bin/python
2# Python to manage netCDF files.
3# From L. Fita work in different places: CCRC (Australia), LMD (France)
4# More information at: http://www.xn--llusfb-5va.cat/python/PyNCplot
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
11## e.g. # nc_var.py -o lonlat_polygon -f wrfout_d01_1995-01-01_00:00:00 -S star.dat -v XLONG,XLAT
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
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
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
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
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
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'
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
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
25## e.g. # nc_var.py -o itime -S WRFtime -f ../PY/wrfout_d01_1995-01-01_00:00:00 -v Times
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
28## e.g. # nc_var.py -o join_singlestation_obsfiles -S 'obs/sfc_CAM:OBSnetcdf' -v all
29## e.g. # nc_var.py -o join_sounding_obsfiles -S .:UWyoming_snd_1 -v all
30## e.g. # nc_var.py -o timemean -f selvar_new.nc -S 2:XLONG,XLAT -v T2
31
32## e.g. ccrc468-17 # ./nc_var.py -v time -f 123/CCRC_NARCliM_Sydney_All_1990-1999_pr10max.nc -o out -S 1:-1
33## e.g. ccrc468-17 # ./nc_var.py -v prac -f xyz/CCRC_NARCliM_Sydney_DAM_1990-1999_prac.nc -o mname -S pluja
34## 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.'
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 addattr -S 'comment|Lluis Fita-123456'
36## 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'
37## 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'
38## 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'
39## e.g. # nc_var.py -o field_stats -f ~/etudes/domains/Polynesie/geo_em.d03.nc -S full -v HGT_M
40## e.g. # nc_var.py -o filter_2dim -S '80,y,x,lon,lat' -f 'tahiti_5m_ll.grd' -v 'z'
41## 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
42## e.g. # nc_var.py -o 'Partialmap_Entiremap' -f carteveg5km.nc -S 'longitude,latitude,std,5000.,Goode,Goode_5km.nc' -v vegetation_map
43## e.g. # nc_var.py -o subbasin -f routing.nc -S Caceres,-57.75,-16.25,left
44## e.g. # nc_var.py -o computevar_model -f ~/PY/wrfout_d01_2001-11-11_00:00:00 -S hurs
45## e.g. # nc_var.py -o model_characteristics -f ~/PY/wrfout_d01_2001-11-11_00:00:00 -S WRF
46## e.g. # nc_var.py -o WRF_toCF -f ~/PY/wrfout_d01_2001-11-11_00:00:00 -S XLONG:XLAT:19491201000000:minutes
47## e.g. # nc_var.py -o cleaning_varsfile -f ~/PY/wrfout_d01_2001-11-11_00:00:00 -S T2,XLONG,XLAT,Times
48## 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'
49## e.g. # nc_var.py -o CDO_toCF -f LMDZ/AR40/hfss_reproj-histins.nc
50## 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
51## 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
52## 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
53## 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'
54## 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'
55## 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
56## e.g. # nc_var.py -o getvars_tofile -S soils_param_Zobler_textXIOS.nc -f soils_param_colorXIOS.nc -v 'soiltext,soiltexttypes'
57## e.g. # nc_var.py -o addVar -S 'lon,lat|mask@mask@1|f' -f new_ORCHIDEE_13PFTmap_2010_cmpi6_LUH2v2h.nc -v mask
58## 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
59## e.g. $ nc_var.py -o VarVal_FillValue -S '0.,eq,std' -f new_lai2D.nc -v LAI
60## e.g. # nc_var.py -o rm_FillValue -f new_ORCHIDEE_13PFTmap_2010_cmpi6_LUH2v2h.nc -S 0 -v mask
61## 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
62## 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'
63## e.g. # nc_var.py -o temporal_stats -S 'Time:WRFtime:day@1@min,LTday@-3@1@min,agghour@1@mean:bottom_top@ZNU,south_north@XLAT,west_east@XLONG' -f wrfout_d01_1995-01-01_00:00:00 -v T2,Q2
64## 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
65## 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
66## e.g. # nc_var.py -o same_deltasign -f wrfout_d01_1995-01-01_00:00:00 -S 'Time:0|south_north:60|west_east:-1' -v T2,Q2,XLAT,XLONG
67## e.g. # nc_var.py -o compute_slices_stats -S 'XLONG,-74.,-36.,4.;XLAT,-62.,18.,2.;HGT,500.,7000.,500.@Time|Times:west_east|XLONG:south_north|XLAT@Time' -f wrfout_d01_1995-01-01_00:00:00 -v T2,Q2
68## e.g. # nc_var.py -o dimrename -f /media/lluis/ExtDiskC_ext3/DATA/estudios/FPS_Alps/additional/IOP/select/out_irene/simcdx_vars_cape_120lev_cdxwrf2.nc -S Time -v time0
69## e.g. # nc_var.py -o area_weighted -f 'reference_data.nc:lon;lon;lon_bnds;-1;lat;lat;lat_bnds;-1,get_data.nc:lon;lon;lon_bnds;-1;lat;lat;lat_bnds;-1' -S 'yes:min,max,mean,stddev,count' -v ct_values,xband_values,box_values,mosaic_values
70## e.g. # nc_var.py -o area_weighted -f '/media/lluis/ExtDiskC_ext4/bkup/llamp/estudios/dominios/SA150k/geo_em.d01.nc:west_east;XLONG_M;WRFxbnds;-1;south_north;XLAT_M;WRFybnds;-1,/media/lluis/ExtDiskC_ext4/bkup/llamp/estudios/dominios/SA50k/geo_em.d01.nc:west_east;XLONG_M;WRFxbnds;-1;south_north;XLAT_M;WRFybnds;-1' -S 'no:mean' -v HGT_M
71## e.g. # nc_var.py -o compute_slices_stats_areaweighted -S 'XLONG,-74.,-36.4,4.;XLAT,-63.,19.,4.;HGT,500.,7000.,500.@Time|WRFtime:west_east|XLONG:south_north|XLAT@Time@west_east|lon_bnds,south_north|lat_bnds@XLONG|lat_bnds;lon_bnds,XLAT|lat_bnds;lon_bnds@Time' -f wrfout_bnds.nc -v T2,U10,V10,Q2
72## e.g. # nc_var.py -o compute_slices_stats_areaweighted -S 'lat,-63.,19.,2.;orog,500.,7000.,500.;rangefaces,fixed,-2.5|-0.5,-0.5|0.5,0.5|2.5@time|time:lon|lon:lat|lat@time@lon|lon_bnds,lat|lat_bnds@lon|lon_bnds,lat|lat_bnds@lat,lon@time' -f /media/lluis/ExtDiskC_ext3/DATA/estudios/Andes/DATA/concatenated/historical/tasmin/tasmin_Amon_ACCESS1-0_historical_r1i1p1_185001-200512_Andes_19600101000000-19900101000000.nc -v tasmin
73## e.g. # nc_var.py -o except_fillValue -S 'orog:range,500.,7000.:None' -f /home/lluis/estudios/Andes/cmip_data/fx/orog_fx_ACCESS1-0_historical_r0i0p0.nc -v 'all'
74## e.g. # nc_var.py -o usefile_compute_slices_stats_areaweighted -S 'compute_slices_stats_areaweighted.nc@XLAT_M-HGT_M-rangefaces@Time|WRFtime:west_east|XLONG_M:south_north|XLAT_M:land_cat|INTrange@Time,land_cat' -f 'geo_em.d01.nc' -v 'LANDUSEF'
75## e.g. # nc_var.py -o compress_data -S 'XLAND:Time|0:single,1:X|west_east|XLONG,Y|south_north|XLAT' -f wrfout_d01_1995-01-01_00:00:00 -v T2,LU_INDEX,Times
76## e.g. # nc_var.py -o CFfile_creation -S 'lon|360,lat|180,time|None@20:global' -v 'tas#time;lat;lon#f#None,time#time#f8#units|seconds!since!1949-12-01!00:00:00|S' -f newCF.nc
77
78from optparse import OptionParser
79import numpy as np
80from netCDF4 import Dataset as NetCDFFile
81import os
82import re
83import nc_var_tools as ncvar
84# Using 'generic_tools.py'
85import generic_tools as gen
86
87# addDim: Operation to add a new dimension in a file
88# addVar: Operation to add a new variable in a file using exisintg dimensions
89# addvals: Function to add values to a given variable at a given dimension
90# area_weighted: Function to provide an area weighted statistics within two different values
91#   of matrices assuming regular lon/lat projections without taking into account Earth's curvature
92# CDO_toCF: Function to pass a CDO output file to CF-conventions
93# CFfile_creation: Operation to create a file folowing CF-conventions
94# CFmorzization: Function to provide a CF-compilation version of a variable within a file
95# chdimname: Changing the name of the dimension
96# changevartype: Function to change the type of a variable (when possible)
97# checkallvars: Function to check all variables of a file
98# checkAllValues: Function to check for variables with along all their dimensions with the same value in a file
99# checkNaNs: Function to check for NaN values over all variables in a file
100# chgtimestep: Function to change the values of a given time-step of a variable inside a netCDF for values from a nother file
101# chvarname: Changing the name of the variable
102# cleaning_varsfile: Function to keep a list of varibales from a file
103# compress_data: Function to compress (only provide values for a criteria) the values of a 2D
104#   file following a given criteria from one of its variables
105# compute_deaccum: Function to compute deaccum: deaccumulation of a variable (VAR[t+1]-VAR[t])
106# compute_opersvarsfiles: Function to compute opersvarfiles: operation of variables from different files
107# compute_opervaralltime: Function to compute opervaralltime: operation of variable successible allover the time-steps
108# compute_opervartimes: Function to compute opervartimes: operation of variable for a given sub-set of time-steps
109# compute_slices_stats: Function to compute stats of variables of a file splitting variables by
110#   slices along sets of ranges for a series of variables
111# compute_slices_stats_areaweighted: Function to compute stats of variables of a file splitting variables by
112#   slices along sets of ranges for a series of variables weighting by the area
113#   covered by each grid (defined as polygon) within the slice
114# compute_slice2Dstats: Function to compute stats of variables of a file following slices along 2 variables
115# compute_tevolboxtraj: Function to compute tevolboxtraj: temporal evolution at a given point along a box following a trajectory
116# computevar_model: Function to provide the way to compute a CF-variable providing its name
117# curve_section: Function to provide a section of a file following a given curve
118# DatesFiles: Function to find different time values on a series of WRF files in a folder
119# DataSetSection: Function to get a section (values along a dimension) of a given data-set
120# DataSetSection_multidims: Function to get a section (values along multiple dimensions) of a given data-set
121# DataSetSection_multivars: Function to get a section (values along multiple variables) of a given data-set
122# DYNAMICO_toCF: Function to pass a DYNAMICO original file to CF-conventions
123# dimrename: Renaming a dimension from a file
124# dimrm: Removing a dimension from a file
125# dimToUnlimited: Operation to create an unlimited dimension from an existing one
126# dimVar_creation: Function to add a 1D variable with the size of a given dimension in a file
127# except_fillValue: Function to fill a file with fill_Value except a given value of a variable
128# fattradd: Adding attributes from a reference file
129# fdimadd: Adding dimension from another reference file
130# fgaddattr: Adding global attributes from a reference file
131# field_stats: Function to retrieve statistics from a field
132# field_stats_dim: Function to retrieve statistics from a field along dimensions
133# file_creation: Operation to create a file with one variable with a given set of dimensions
134# file_oper_alongdims: Function to operate a file along different dimensions of a variable
135# filter_2dim: Function to filter along 2 dimensions (moving grid-box means of a given size) values of the netCDF file
136# flipdim: flips the value following one dimension
137# fvaradd: Adding variable (and all its attributes and dimensions) from a reference file to a file
138# gaddattrk: Add a global attribute to a netCDF caring about the type. Removes previous attribute if it exist
139# gaddattr: Add a global attribute to a netCDF. Removes previous attribute if it exist
140# get_attribute: Function to get an attribute from a netCDF file
141# get_point: Function to provide the closest grid point to a given lat,lon
142# get_time: Function to provide the closest time-step to a given time
143# get_namelist_vars: Function to get namelist-like  values ([varname] = [value])
144# get_Variables: Function to get a list of variables from an existing file
145# getvalues_lonlat: Function to retrieve the values from the closest grid point to a set of longitude, latitude values
146# getvars_tofile: Function to get variables from a file and pass them to another one
147# grattr: Function to read a global atribute
148# grmattr: Removing a global attribute
149# idims: Give all the dimensions names of a file
150# ifile: Function to provide some information from a given file
151# igattrs: Give all the global attributes of a file
152# increaseDimvar: Function to increase with 1 dimension an existing variable within a netcdf file. Values of
153#   the variable will be repeated along the new dimension
154# isgattrs: Give a single global attribute of a file and its type
155# isvattrs: Give a single attribute of a variable
156# itime: Function to provide information of the time from a netCDF file
157# ivars: Give all the variable names of a file
158# ivattrs: Give all the attributes of a variable and its type
159# join_singlestation_obsfiles: Function to join files from 'single-station'
160#   `create_OBSnetcdf.py' script to create a single file
161# join_sounding_obsfiles: Function to join 1D variables from files generated by
162#   `UWyoming_snd_nc.py' script to create a single file
163# LMDZ_toCF: Function to pass a LMDZ original file to CF-conventions
164# lonlat_polygon: Function to define a lon/lat region giving the coordinates of the vertexs of a given polygon
165# 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)
166# merge_files: Function to merge variables from two files
167# model_characteristics: Function to provide major characterisitcs of a given model output
168# mthDYNAMICO_toCF: Function to pass a mthDYNAMICO original file to CF-conventions
169# ncreplace: Function to replace something from a netCDF file
170# ncstepdiff: Function to compute differencies between time-steps (deacumulate) a netCDF file
171# netcdf_concatenation: Function to concatenate netCDF files for a given set of variables
172# netcdf_fold_concatenation: Function to concatenate netCDF files in a given folder for a given set of variables
173# netcdf_fold_concatenation_HMT: Function to concatenate netCDF files in a given folder for a given set of variables
174#   giving Header, Middle, Tail for the name files
175# reconstruct_matrix_from_vector: Function to reconstruct a 2D matrix from a pair of syncronized vectors with the positions on x and y coordinates
176# reproject: Function to reproject values to another one
177# rm_FillValue: Operation to remove the _FillValue from a variable inside a netCDF file
178# Partialmap_Entiremap: Function to transform from a partial global map (e.g.: only land points) to an entire one
179#   Coincidence of points is done throughout a first guess from fractions of the total domain of search
180# Partialmap_EntiremapFor: Function to transform from a partial global map (e.g.: only land points) to an entire one
181#   using Fortran code Coincidence of points is done throughout a first guess from fractions of the total domain of search
182# Partialmap_EntiremapForExact: Function to transform from a partial global map (e.g.: only land points) to an entire
183#   one using Fortran code with exact location Coincidence of points is done throughout a first guess from fractions of
184#   the total domain of search
185# pinterp: Function to vertically interpolate using subroutines from the p_interp.F90 NCAR program
186# remapnn: Function to remap to the nearest neightbor a variable using projection from another file
187# retrieve_stations: Function to retrieve temporal values at given stations provided by a secondary netcdf
188# same_deltasign: Function to determine if a given series of 1D values share the same sign of
189#   increase/decrease between consecutive values
190# seasmean: Function to compute the seasonal mean of a variable
191# sellonlatbox: Function to select a lotlan box from a data-set
192# sellonlatlevbox: Function to select a lotlan box and a given level from a data-set
193# selvar: Function to select a series of variables from a netcdf file. Variables with
194# setvar_asciivalues: Function to set de values of a variable with an ASCII file (common Fortran-like format)
195# setvar_nc: Operation to set values of a variable from values of an other one
196# sorttimesmat: Function to sort the time values of a given file
197# spacemean: Function to retrieve a space mean series from a multidimensional variable of a file
198# SpatialWeightedMean: Function to compute the spatial mean using weights from a netCDF file
199# 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)
200# statcompare_files: Python script to statistically compare two different files
201# subbasin: Function to retrieve the subbasin (all the sub-flows untila a given lon,lat)
202# submns: Function to retrieve a series of months from a file
203# subyrs: Function to retrieve a series of years from a file
204# temporal_stats: Function to compute temporal statistics. Rank of the variables are
205#   preserved along other non-temporal dimensions
206# TimeInf: Function to print all the information from the variable time
207# time_reset: Function to re-set the time axis of a file
208# TimeSplitmat: Function to transform a file with CFtimes to a matrix [Nyear,Nmonth,Nday,Nhour,Nminute,Nsecond]
209# timemean: Function to retrieve a time mean series from a multidimensional variable of a file
210# usefile_compute_slices_stats_areaweighted: Function to compute stats of variables of
211#   a file splitting variables by slices along sets of ranges for a series of
212#   variables weighting by the area covered by each grid (defined as polygon) within
213#   the slice using pre-calculated area-weights from an existing file
214# valmod: Function to modify the value of a variable
215# valmod_dim: Function to modify the value of a variable at a given dimension and value
216# varaddattrk: Add an attribute to a variable caring about the type
217# varaddattr: Add an attribute to a variable. Removes previous attribute if it exists
218# varaddref: Function to add a variable in an existing file copying characteristics from an existing one
219# var_creation: Operation to create a new variable in a file with a given set of dimensions
220# varout: Function when we want to output variable values
221# varrmattr: Removing an attribute from a variable
222# varrm: Removing a variable from a file
223# VarVal_FillValue: Function to transform a given value from a given variable to _FillValue in a netCDF file
224# vrattr: Function to remove an atribute from a variable
225# WRF_d0Nref: Function for the generation of an extra WRF domain from a given one
226# WRF_CFlonlat_creation: Function to add a CF-convention longitude/latitude variables in a WRF file
227# WRF_CFtime_creation: Function to add a CF-convention time unit in a WRF file
228# WRF_CFxtime_creation: Function to add a CF-convention time unit in a WRF file using variable 'XTIME'
229# WRF_toCF: Function to pass a WRF original file to CF-conventions
230# WRF_to_newCF: Function to pass a WRF original file to new CF-conventions file
231
232operations=['addDim', 'addVar', 'addvals', 'area_weighted', 'CDO_toCF',              \
233  'CFfile_creation', 'CFmorzization', 'chdimname', 'changevartype',                  \
234  'checkallvars', 'checkAllValues', 'checkNaNs',                                     \
235  'chgtimestep', 'chvarname', 'cleaning_varsfile', 'compress_data',                  \
236  'compute_deaccum', 'compute_opersvarsfiles',                                       \
237  'compute_opervaralltime', 'compute_opervartimes', 'compute_slices_stats',          \
238  'compute_slices_stats_areaweighted', 'compute_slice2Dstats',                       \
239  'compute_tevolboxtraj',                                                            \
240  'computevar_model', 'curve_section', 'DatesFiles',                                 \
241  'DataSetSection', 'DataSetSection_multidims', 'DataSetSection_multivars',          \
242  'DYNAMICO_toCF', 'dimrename', 'dimrm', 'dimToUnlimited', 'dimVar_creation',        \
243  'except_fillValue', 'fattradd',                                                    \
244  'fdimadd', 'fgaddattr', 'field_stats', 'field_stats_dim', 'file_creation',         \
245  'file_oper_alongdims', 'filter_2dim',                                              \
246  'flipdim', 'fvaradd', 'gaddattrk', 'gaddattr', 'get_attribute',                    \
247  'get_point', 'get_time', 'get_namelist_vars', 'get_Variables',                     \
248  'getvalues_lonlat', 'getvars_tofile', 'grattr',                                    \
249  'grmattr', 'idims', 'ifile', 'igattrs', 'increaseDimvar', 'isgattrs',              \
250  'isvattrs', 'itime', 'ivars', 'ivattrs', 'join_singlestation_obsfiles',            \
251  'join_sounding_obsfiles', 'LMDZ_toCF', 'lonlat_polygon', 'maskvar',                \
252  'merge_files', 'model_characteristics',                                            \
253  'mthDYNAMICO_toCF', 'ncreplace', 'ncstepdiff', 'netcdf_concatenation',             \
254  'netcdf_fold_concatenation',                                                       \
255  'netcdf_fold_concatenation_HMT', 'reproject', 'Partialmap_Entiremap',              \
256  'Partialmap_EntiremapFor', 'Partialmap_EntiremapForExact',                         \
257  'pinterp', 'reconstruct_matrix_from_vector', 'remapnn', 'retrieve_stations',       \
258  'rm_FillValue', 'same_deltasign',                                                  \
259  'seasmean', 'sellonlatbox', 'sellonlatlevbox', 'selvar', 'setvar_asciivalues',     \
260  'setvar_nc', 'sorttimesmat', 'spacemean', 'SpatialWeightedMean',                   \
261  'splitfile_dim', 'statcompare_files',                                              \
262  'subbasin', 'submns', 'subyrs', 'temporal_stats', 'TimeInf', 'time_reset',         \
263  'TimeSplitmat', 'timemean', 'usefile_compute_slices_stats_areaweighted',           \
264  'valmod', 'valmod_dim','varaddattrk', 'varaddattr',                                \
265  'varaddref',                                                                       \
266  'var_creation', 'varout', 'varoutold', 'varrmattr', 'varrm', 'VarVal_FillValue',   \
267  'vrattr', 'WRF_d0Nref',                                                            \
268  'WRF_CFlonlat_creation', 'WRF_CFtime_creation', 'WRF_CFxtime_creation',            \
269  'list_operations', 'WRF_toCF', 'WRF_to_newCF']
270
271### Options
272##string_operation="operation to make: " + '\n' + " out, output values -S inidim1,[inidim2,...]:enddim1,[enddim2,...]"
273string_operation="""operation to make:
274  addgattr, add a new global attribute: addatr -S [attrname]|[attrvalue]
275  addvattr, add a new attribute to any given variable: addatr -S [attrname]|[attrvalue]
276  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
277  checkallvalrs: Function to check all variables of a file: -S [dimn1],[[dimn2],...,[dimnN]]:[dim1],[[dim2],...,[dimN]]
278  mname, modify name -S newname
279  out, output values -S inidim1,[inidim2,...]:enddim1,[enddim2,...]
280  valmod, modifiy values of variable -S [modification]:
281     sumc,[constant]: add [constant] to variables values
282     subc,[constant]: substract [constant] to variables values
283     mulc,[constant]: multipy by [constant] to variables values
284     divc,[constant]: divide by [constant] to variables values
285  rmgattr, remove a global attribute: rmgattr -S [attrname]
286  rmvattr, remove an attribute to any given variable: rmvattr -S [attrname]
287"""
288
289#print string_operation
290
291operationnames = "'" + gen.numVector_String(operations, "', '") + "'"
292
293parser = OptionParser()
294parser.add_option("-f", "--netCDF_file", dest="ncfile", help="file to use", 
295  metavar="FILE")
296parser.add_option("-o", "--operation", type='choice', dest="operation", 
297  choices=operations, help="operation to make: " + operationnames, metavar="OPER")
298parser.add_option("-S", "--valueS", dest="values", 
299  help="values to use according to the operation (when applicable); '-h' specific help of the operation", metavar="VALUES")
300parser.add_option("-v", "--variable", dest="varname",
301  help="variable to use (when applicable)", metavar="VAR")
302
303(opts, args) = parser.parse_args()
304
305#if opts.help:
306#  parser.print_help()
307#  print string_operation
308#  sys.exit()
309
310#######    #######
311## MAIN
312    #######
313
314# Operations which file name is not a real file
315NotCheckingFile = ['area_weighted', 'CFfile_creation','DatesFiles',                  \
316  'compute_opersvarsfiles', 'file_creation',                                         \
317  'join_singlestation_obsfiles', 'join_sounding_obsfiles', 'list_operations',        \
318  'merge_files',                                                                     \
319  'model_characteristics', 'netcdf_concatenation', 'netcdf_fold_concatenation',      \
320  'netcdf_fold_concatenation_HMT']
321
322####### ###### ##### #### ### ## #
323errormsg='ERROR -- error -- ERROR -- error'
324
325varn=opts.varname
326oper=opts.operation
327
328if opts.operation is None:
329    print errormsg
330    print '  No operation provided !!'
331    print "  an operation must be provided as '-o [operationname]' "
332    quit(-1)
333
334if opts.ncfile is not None and not os.path.isfile(opts.ncfile) and                   \
335  not gen.searchInlist(NotCheckingFile,oper) and opts.ncfile != 'h':
336    print errormsg
337    print "  File '" + opts.ncfile + "' does not exist !!"
338    quit(-1)
339elif opts.ncfile is None and not gen.searchInlist(NotCheckingFile,oper) and          \
340  opts.values != 'h':
341    print errormsg
342    print '  No file provided !!'
343    print "  a file must be provided as '-f [filename]' "
344    quit(-1)
345
346if oper == 'addDim':
347    ncvar.addDim(opts.values, opts.ncfile, opts.varname)
348elif oper == 'addVar':
349    ncvar.addVar(opts.values, opts.ncfile, opts.varname)
350elif oper == 'addvals':
351    ncvar.addvals(opts.values, opts.ncfile, opts.varname)
352elif oper == 'area_weighted':
353    ncvar.area_weighted(opts.values, opts.ncfile, opts.varname)
354elif oper == 'CDO_toCF':
355    ncvar.CDO_toCF(opts.ncfile)
356elif oper == 'CFfile_creation':
357    ncvar.CFfile_creation(opts.values, opts.ncfile, opts.varname)
358elif oper == 'CFmorzization':
359    ncvar.CFmorzization(opts.values, opts.ncfile, opts.varname)
360elif oper == 'chdimname':
361    ncvar.chdimname(opts.values, opts.ncfile)
362elif oper == 'changevartype':
363    ncvar.changevartype(opts.values, opts.ncfile, opts.varname)
364elif oper == 'checkallvars':
365    ncvar.checkallvars(opts.values, opts.ncfile)
366elif oper == 'checkAllValues':
367    ncvar.checkAllValues(opts.values, opts.ncfile)
368elif oper == 'checkNaNs':
369    ncvar.checkNaNs(opts.values, opts.ncfile)
370elif oper == 'chgtimestep':
371    ncvar.chgtimestep(opts.values, opts.ncfile, opts.varname)
372elif oper == 'chvarname':
373    ncvar.chvarname(opts.values, opts.ncfile, opts.varname)
374elif oper == 'cleaning_varsfile':
375    ncvar.cleaning_varsfile(opts.values, opts.ncfile)
376elif oper == 'compress_data':
377    ncvar.compress_data(opts.values, opts.ncfile, opts.varname)
378elif oper == 'compute_deaccum':
379    ncvar.compute_deaccum(opts.values, opts.ncfile, opts.varname)
380elif oper == 'compute_opersvarsfiles':
381    ncvar.compute_opersvarsfiles(opts.values, opts.varname)
382elif oper == 'compute_opervaralltime':
383    ncvar.compute_opervaralltime(opts.values, opts.ncfile, opts.varname)
384elif oper == 'compute_opervartimes':
385    ncvar.compute_opervartimes(opts.values, opts.ncfile, opts.varname)
386elif oper == 'compute_slices_stats':
387    ncvar.compute_slices_stats(opts.values, opts.ncfile, opts.varname)
388elif oper == 'compute_slices_stats_areaweighted':
389    ncvar.compute_slices_stats_areaweighted(opts.values, opts.ncfile, opts.varname)
390elif oper == 'compute_slice2Dstats':
391    ncvar.compute_slice2Dstats(opts.values, opts.ncfile, opts.varname)
392elif oper == 'compute_tevolboxtraj':
393    ncvar.compute_tevolboxtraj(opts.values, opts.ncfile, opts.varname)
394elif oper == 'computevar_model':
395    ncvar.computevar_model(opts.values, opts.ncfile)
396elif oper == 'curve_section':
397    ncvar.curve_section(opts.values, opts.ncfile, opts.varname)
398elif oper == 'DataSetSection':
399    ncvar.DataSetSection(opts.values, opts.ncfile)
400elif oper == 'DataSetSection_multidims':
401    ncvar.DataSetSection_multidims(opts.values, opts.ncfile, opts.varname)
402elif oper == 'DataSetSection_multivars':
403    ncvar.DataSetSection_multivars(opts.values, opts.ncfile, opts.varname)
404elif oper == 'DatesFiles':
405    ncvar.DatesFiles(opts.values, opts.ncfile, opts.varname)
406elif oper == 'DYNAMICO_toCF':
407    ncvar.DYNAMICO_toCF(opts.values, opts.ncfile)
408elif oper == 'dimrename':
409    ncvar.dimrename(opts.ncfile, opts.values, opts.varname)
410elif oper == 'dimrm':
411    ncvar.dimrm(opts.ncfile, opts.values, opts.varname)
412elif oper == 'dimToUnlimited':
413    ncvar.dimToUnlimited(opts.values, opts.ncfile)
414elif oper == 'dimVar_creation':
415    ncvar.dimVar_creation(opts.values, opts.ncfile)
416elif oper == 'except_fillValue':
417    ncvar.except_fillValue(opts.values, opts.ncfile, opts.varname)
418elif oper == 'fattradd':
419    ncvar.fattradd(var, opts.values, opts.ncfile)
420elif oper == 'fdimadd':
421    ncvar.fdimadd(opts.values, opts.ncfile)
422elif oper == 'fgaddattr':
423    ncvar.fgaddattr(opts.values, opts.ncfile)
424elif oper == 'file_creation':
425    ncvar.file_creation(opts.values, opts.ncfile, opts.varname)
426elif oper == 'file_oper_alongdims':
427    ncvar.file_oper_alongdims(opts.values, opts.ncfile, opts.varname)
428elif oper == 'field_stats':
429    ncvar.field_stats(opts.values, opts.ncfile, opts.varname)
430elif oper == 'field_stats_dim':
431    ncvar.field_stats_dim(opts.values, opts.ncfile, opts.varname)
432elif oper == 'filter_2dim':
433    ncvar.filter_2dim(opts.values, opts.ncfile, opts.varname)
434elif oper == 'flipdim':
435    ncvar.flipdim(opts.values, opts.ncfile, opts.varname)
436elif oper == 'fvaradd':
437    ncvar.fvaradd(opts.values, opts.ncfile)
438elif oper == 'gaddattrk':
439    ncvar.gaddattrk(opts.values, opts.ncfile)
440elif oper == 'gaddattr':
441    ncvar.gaddattr(opts.values, opts.ncfile)
442elif oper == 'get_attribute':
443    ncvar.get_attribute(opts.values, opts.ncfile, opts.varname)
444elif oper == 'get_namelist_vars':
445    ncvar.get_namelist_vars(opts.values, opts.ncfile)
446elif oper == 'get_point':
447    ncvar.get_point(opts.values, opts.ncfile, opts.varname)
448elif oper == 'get_time':
449    ncvar.get_time(opts.values, opts.ncfile, opts.varname)
450elif oper == 'get_Variables':
451    ncvar.get_Variables(opts.values, opts.ncfile, opts.varname)
452elif oper == 'getvalues_lonlat':
453    ncvar.getvalues_lonlat(opts.values, opts.ncfile)
454elif oper == 'getvars_tofile':
455    ncvar.getvars_tofile(opts.values, opts.ncfile, opts.varname)
456elif oper == 'grattr':
457    ncvar.grattr(opts.values, opts.ncfile)
458elif oper == 'grmattr':
459    ncvar.grmattr(opts.values, opts.ncfile)
460elif oper == 'idims':
461    ncvar.idims(opts.ncfile)
462elif oper == 'ifile':
463    ncvar.ifile(opts.ncfile)
464elif oper == 'igattrs':
465    ncvar.igattrs(opts.ncfile)
466elif oper == 'increaseDimvar':
467    ncvar.increaseDimvar(opts.values, opts.ncfile, opts.varname)
468elif oper == 'isgattrs':
469    ncvar.isgattrs(opts.values, opts.ncfile)
470elif oper == 'isvattrs':
471    ncvar.isvattrs(opts.values, opts.ncfile, opts.varname)
472elif oper == 'itime':
473    ncvar.itime(opts.values, opts.ncfile, opts.varname)
474elif oper == 'ivars':
475    ncvar.ivars(opts.ncfile)
476elif oper == 'ivattrs':
477    ncvar.ivattrs(opts.ncfile, opts.varname)
478elif oper == 'join_singlestation_obsfiles':
479    ncvar.join_singlestation_obsfiles(opts.values, opts.varname)
480elif oper == 'join_sounding_obsfiles':
481    ncvar.join_sounding_obsfiles(opts.values, opts.varname)
482elif oper == 'list_operations':
483# From: http://www.diveintopython.net/power_of_introspection/all_together.html
484    object = ncvar
485    for opern in operations:
486        if  opern != 'list_operations': 
487            print opern + '_______ ______ _____ ____ ___ __ _'
488            print getattr(object, opern).__doc__
489elif oper == 'LMDZ_toCF':
490    ncvar.LMDZ_toCF(opts.values, opts.ncfile)
491elif oper == 'lonlat_polygon':
492    ncvar.lonlat_polygon(opts.values, opts.ncfile, opts.varname)
493elif oper == 'maskvar':
494    ncvar.maskvar(opts.values, opts.ncfile, opts.varname)
495elif oper == 'merge_files':
496    ncvar.merge_files(opts.values, opts.ncfile, opts.varname)
497elif oper == 'model_characteristics':
498    ncvar.model_characteristics(opts.values, opts.ncfile)
499elif oper == 'mthDYNAMICO_toCF':
500    ncvar.mthDYNAMICO_toCF(opts.values, opts.ncfile)
501elif oper == 'ncreplace':
502    ncvar.ncreplace(opts.values, opts.ncfile, opts.varname)
503elif oper == 'ncstepdiff':
504    ncvar.ncstepdiff(opts.values, opts.ncfile, opts.varname)
505elif oper == 'netcdf_concatenation':
506    ncvar.netcdf_concatenation(opts.ncfile)
507elif oper == 'netcdf_fold_concatenation':
508    ncvar.netcdf_fold_concatenation(opts.values, opts.ncfile, opts.varname)
509elif oper == 'netcdf_fold_concatenation_HMT':
510    ncvar.netcdf_fold_concatenation_HMT(opts.values, opts.ncfile, opts.varname)
511elif oper == 'opersvarsfiles':
512    ncvar.compute_opersvarsfiles(opts.values, opts.varname)
513elif oper == 'pinterp':
514    ncvar.pinterp(opts.values, opts.ncfile, opts.varname)
515elif oper == 'remapnn':
516    ncvar.remapnn(opts.values, opts.ncfile, opts.varname)
517elif oper == 'Partialmap_Entiremap':
518    ncvar.Partialmap_Entiremap(opts.values, opts.ncfile, opts.varname)
519elif oper == 'Partialmap_EntiremapFor':
520    ncvar.Partialmap_EntiremapFor(opts.values, opts.ncfile, opts.varname)
521elif oper == 'Partialmap_EntiremapForExact':
522    ncvar.Partialmap_EntiremapForExact(opts.values, opts.ncfile, opts.varname)
523elif oper == 'reconstruct_matrix_from_vector':
524    ncvar.reconstruct_matrix_from_vector(opts.values, opts.ncfile, opts.varname)
525elif oper == 'reproject':
526    ncvar.reproject(opts.values, opts.ncfile, opts.varname)
527elif oper == 'retrieve_stations':
528    ncvar.retrieve_stations(opts.values, opts.ncfile, opts.varname)
529elif oper == 'rm_FillValue':
530    ncvar.rm_FillValue(opts.values, opts.ncfile, opts.varname)
531elif oper == 'same_deltasign':
532    ncvar.same_deltasign(opts.values, opts.ncfile, opts.varname)
533elif oper == 'seasmean':
534    ncvar.seasmean(timename, opts.ncfile, opts.varname)
535elif oper == 'sellonlatbox':
536    ncvar.sellonlatbox(opts.values, opts.ncfile, opts.varname)
537elif oper == 'sellonlatlevbox':
538    ncvar.sellonlatlevbox(opts.values, opts.ncfile, opts.varname)
539elif oper == 'selvar':
540    ncvar.selvar(opts.values, opts.ncfile, opts.varname)
541elif oper == 'setvar_asciivalues':
542    ncvar.setvar_asciivalues(opts.values, opts.ncfile, opts.varname)
543elif oper == 'setvar_nc':
544    ncvar.setvar_nc(opts.values, opts.ncfile, opts.varname)
545elif oper == 'sorttimesmat':
546    ncvar.sorttimesmat(opts.ncfile, opts.varname)
547elif oper == 'spacemean':
548    ncvar.spacemean(opts.ncfile, opts.varname)
549elif oper == 'SpatialWeightedMean':
550    ncvar.SpatialWeightedMean(opts.values, opts.ncfile, opts.varname)
551elif oper == 'splitfile_dim':
552    ncvar.splitfile_dim(opts.values, opts.ncfile, opts.varname)
553elif oper == 'statcompare_files':
554    ncvar.statcompare_files(opts.values)
555elif oper == 'subbasin':
556    ncvar.subbasin(opts.values, opts.ncfile)
557elif oper == 'submns':
558    ncvar.submns(opts.values, opts.ncfile, opts.varname)
559elif oper == 'subyrs':
560    ncvar.subyrs(opts.values, opts.ncfile, opts.varname)
561elif oper == 'temporal_stats':
562    ncvar.temporal_stats(opts.values, opts.ncfile, opts.varname)
563elif oper == 'TimeInf':
564    ncvar.TimeInf(opts.ncfile, opts.varname)
565elif oper == 'time_reset':
566    ncvar.time_reset(opts.values, opts.ncfile, opts.varname)
567elif oper == 'TimeSplitmat':
568    ncvar.TimeSplitmat(opts.values, opts.ncfile, opts.varname)
569elif oper == 'timemean':
570    ncvar.timemean(opts.values, opts.ncfile, opts.varname)
571elif oper == 'usefile_compute_slices_stats_areaweighted':
572    ncvar.usefile_compute_slices_stats_areaweighted(opts.values, opts.ncfile,        \
573      opts.varname)
574elif oper == 'valmod':
575    ncvar.valmod(opts.values, opts.ncfile, opts.varname)
576elif oper == 'valmod_dim':
577    ncvar.valmod_dim(opts.values, opts.ncfile, opts.varname)
578elif oper == 'varaddattrk':
579    ncvar.varaddattrk(opts.values, opts.ncfile, opts.varname)
580elif oper == 'varaddattr':
581    ncvar.varaddattr(opts.values, opts.ncfile, opts.varname)
582elif oper == 'varaddref':
583    ncvar.varaddref(opts.values, opts.ncfile, opts.varname)
584elif oper == 'var_creation':
585    ncvar.var_creation(opts.values, opts.ncfile, opts.varname)
586elif oper == 'varout':
587    ncvar.varout(opts.values, opts.ncfile, opts.varname)
588elif oper == 'varoutold':
589    ncvar.varoutold(opts.values, opts.ncfile, opts.varname)
590elif oper == 'varrmattr':
591    ncvar.varrmattr(opts.values, opts.ncfile, opts.varname)
592elif oper == 'varrm':
593    ncvar.varrm(opts.ncfile, opts.varname)
594elif oper == 'VarVal_FillValue':
595    ncvar.VarVal_FillValue(opts.values, opts.ncfile, opts.varname)
596elif oper == 'vrattr':
597    ncvar.vrattr(opts.values, opts.ncfile, opts.varname)
598elif oper == 'WRF_d0Nref':
599    ncvar.WRF_d0Nref(opts.values, opts.ncfile)
600elif oper == 'WRF_CFlonlat_creation':
601    ncvar.WRF_CFlonlat_creation(opts.values, opts.ncfile, opts.varname)
602elif oper == 'WRF_CFtime_creation':
603    ncvar.WRF_CFtime_creation(opts.values, opts.ncfile, opts.varname)
604elif oper == 'WRF_CFxtime_creation':
605    ncvar.WRF_CFxtime_creation(opts.values, opts.ncfile, opts.varname)
606elif oper == 'WRF_toCF':
607    ncvar.WRF_toCF(opts.values, opts.ncfile)
608elif oper == 'WRF_to_newCF':
609    ncvar.WRF_to_newCF(opts.values, opts.ncfile, opts.varname)
610else:
611    print errormsg
612    print '   The operation ' + oper + ' is not ready !!'
613    print errormsg
614    quit()
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