| 1 |
roquet |
1.7 |
function []=MITprof_create(fileOut,nProf,prof_depth,varargin) |
| 2 |
gforget |
1.1 |
%function: MITprof_create |
| 3 |
roquet |
1.7 |
%object: create a file in the "MIT format". Low-level function. |
| 4 |
gforget |
1.1 |
%author: Gael Forget (gforget@mit.edu) |
| 5 |
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%date: june 21th, 2006 |
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% |
| 7 |
roquet |
1.7 |
%usage: [MITprof]=MITprof_create(fileOut,nProf,prof_depth); |
| 8 |
gforget |
1.11 |
% create an empty MITprof netcdf file |
| 9 |
roquet |
1.7 |
% vertical depth levels are set according to prof_depth |
| 10 |
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% create empty variables for all usual T/S fields |
| 11 |
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% |
| 12 |
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% [MITprof]=MITprof_create(fileOut,nProf,prof_depth,list_vars); |
| 13 |
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% same but specifying the list of variables in list_vars cell |
| 14 |
gforget |
1.1 |
% array (e.g. list_vars={'prof_T','prof_Tweight'}). |
| 15 |
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% |
| 16 |
gforget |
1.4 |
%inputs: fileOut data file name |
| 17 |
roquet |
1.7 |
% nProf number of profiles |
| 18 |
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% prof_depth vector of depth levels |
| 19 |
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% list_vars variable list (optional) |
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gforget |
1.1 |
% |
| 21 |
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| 22 |
roquet |
1.7 |
|
| 23 |
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% check that file exists and add prefix and suffix if necessary |
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[pathstr, name, ext] = fileparts(fileOut); |
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if isempty(pathstr) | strcmp(pathstr,'.'), pathstr=pwd; end |
| 26 |
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if isempty(ext) | ~strcmp(ext,'.nc'), ext='.nc'; end |
| 27 |
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fileOut=[pathstr '/' name ext]; |
| 28 |
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| 29 |
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%define netcdf dimensions : |
| 30 |
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nLev=length(prof_depth); |
| 31 |
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prof_depth=reshape(prof_depth,length(prof_depth),1); |
| 32 |
gforget |
1.12 |
iPROF=nProf; iDEPTH=nLev; iINTERP=1; |
| 33 |
roquet |
1.7 |
lTXT=30; fillval=double(-9999); |
| 34 |
gforget |
1.1 |
|
| 35 |
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%=============list of variables that will actually be in the file==============% |
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gforget |
1.11 |
if nargin>3; |
| 37 |
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list_vars=varargin{1}; |
| 38 |
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else; |
| 39 |
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list_vars={'prof_depth','prof_descr','prof_date','prof_YYYYMMDD','prof_HHMMSS',... |
| 40 |
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'prof_lon','prof_lat','prof_basin','prof_point','prof_flag','prof_T','prof_Tweight','prof_Testim','prof_Terr','prof_Tflag',... |
| 41 |
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'prof_S','prof_Sweight','prof_Sestim','prof_Serr','prof_Sflag','prof_D','prof_Destim'}; |
| 42 |
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end; |
| 43 |
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gforget |
1.1 |
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roquet |
1.7 |
% eliminate doublons |
| 46 |
gforget |
1.11 |
[list,m]=unique(list_vars); |
| 47 |
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list_vars=list_vars(sort(m)); |
| 48 |
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| 49 |
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list_vars_plus={}; |
| 50 |
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for ii=1:length(list_vars); |
| 51 |
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if ~isempty(strfind(list_vars{ii},'estim'))&... |
| 52 |
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~strcmp(list_vars{ii},'prof_Testim')&... |
| 53 |
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~strcmp(list_vars{ii},'prof_Sestim'); |
| 54 |
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list_vars_plus={list_vars_plus{:},list_vars{ii}(1:end-5)}; |
| 55 |
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end; |
| 56 |
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end; |
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roquet |
1.7 |
|
| 58 |
gforget |
1.1 |
%==========masters table of variables, units, names and dimensions=============% |
| 59 |
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| 60 |
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mt_v={'prof_depth'}; mt_u={'me'}; mt_n={'depth'}; mt_d={'iDEPTH'}; |
| 61 |
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%mt_v=[mt_v '']; mt_u=[mt_u ' ']; mt_n=[mt_n '']; mt_d=[mt_d '']; |
| 62 |
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mt_v=[mt_v 'prof_date']; mt_u=[mt_u ' ']; mt_n=[mt_n 'Julian day since Jan-1-0000']; mt_d=[mt_d 'iPROF']; |
| 63 |
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mt_v=[mt_v 'prof_YYYYMMDD']; mt_u=[mt_u ' ']; mt_n=[mt_n 'year (4 digits), month (2 digits), day (2 digits)']; mt_d=[mt_d 'iPROF']; |
| 64 |
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mt_v=[mt_v 'prof_HHMMSS']; mt_u=[mt_u ' ']; mt_n=[mt_n 'hour (2 digits), minute (2 digits), second (2 digits)']; mt_d=[mt_d 'iPROF']; |
| 65 |
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mt_v=[mt_v 'prof_lon']; mt_u=[mt_u ' ']; mt_n=[mt_n 'Longitude (degree East)']; mt_d=[mt_d 'iPROF']; |
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mt_v=[mt_v 'prof_lat']; mt_u=[mt_u ' ']; mt_n=[mt_n 'Latitude (degree North)']; mt_d=[mt_d 'iPROF']; |
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mt_v=[mt_v 'prof_basin']; mt_u=[mt_u ' ']; mt_n=[mt_n 'ocean basin index (ecco 4g)']; mt_d=[mt_d 'iPROF']; |
| 68 |
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mt_v=[mt_v 'prof_point']; mt_u=[mt_u ' ']; mt_n=[mt_n 'grid point index (ecco 4g)']; mt_d=[mt_d 'iPROF']; |
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gforget |
1.9 |
mt_v=[mt_v 'prof_flag']; mt_u=[mt_u ' ']; mt_n=[mt_n 'flag = i > 0 for suspicious profile ']; mt_d=[mt_d 'iPROF']; |
| 70 |
gforget |
1.1 |
% |
| 71 |
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mt_v=[mt_v 'prof_T']; mt_u=[mt_u 'degree C']; mt_n=[mt_n 'potential temperature']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 72 |
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mt_v=[mt_v 'prof_Tweight']; mt_u=[mt_u '(degree C)^-2']; mt_n=[mt_n 'pot. temp. least-square weight']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 73 |
gforget |
1.2 |
mt_v=[mt_v 'prof_Testim']; mt_u=[mt_u 'degree C']; mt_n=[mt_n 'pot. temp. estimate (e.g. from atlas)']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 74 |
gforget |
1.1 |
mt_v=[mt_v 'prof_Terr']; mt_u=[mt_u 'degree C']; mt_n=[mt_n 'pot. temp. instrumental error']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 75 |
gforget |
1.2 |
mt_v=[mt_v 'prof_Tflag']; mt_u=[mt_u ' ']; mt_n=[mt_n 'flag = i > 0 means test i rejected data.']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 76 |
gforget |
1.1 |
% |
| 77 |
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mt_v=[mt_v 'prof_S']; mt_u=[mt_u 'psu']; mt_n=[mt_n 'salinity']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 78 |
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mt_v=[mt_v 'prof_Sweight']; mt_u=[mt_u '(psu)^-2']; mt_n=[mt_n 'salinity least-square weight']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 79 |
gforget |
1.2 |
mt_v=[mt_v 'prof_Sestim']; mt_u=[mt_u 'psu']; mt_n=[mt_n 'salinity estimate (e.g. from atlas)']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 80 |
gforget |
1.1 |
mt_v=[mt_v 'prof_Serr']; mt_u=[mt_u 'psu']; mt_n=[mt_n 'salinity instrumental error']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 81 |
gforget |
1.2 |
mt_v=[mt_v 'prof_Sflag']; mt_u=[mt_u ' ']; mt_n=[mt_n 'flag = i > 0 means test i rejected data.']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 82 |
gforget |
1.1 |
% |
| 83 |
gforget |
1.11 |
for ii=1:length(list_vars_plus); |
| 84 |
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mt_v=[mt_v list_vars_plus{ii}]; mt_u=[mt_u 'unknown']; mt_n=[mt_n 'unknown']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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mt_v=[mt_v [list_vars_plus{ii} 'weight']]; mt_u=[mt_u '(unknown)^-2']; mt_n=[mt_n 'unknown least-square weight']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 86 |
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mt_v=[mt_v [list_vars_plus{ii} 'estim']]; mt_u=[mt_u 'unknown']; mt_n=[mt_n 'unknown estimate (e.g. from atlas)']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 87 |
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mt_v=[mt_v [list_vars_plus{ii} 'err']]; mt_u=[mt_u 'unknown']; mt_n=[mt_n 'unknown instrumental error']; mt_d=[mt_d 'iPROF,iDEPTH']; |
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mt_v=[mt_v [list_vars_plus{ii} 'flag']]; mt_u=[mt_u ' ']; mt_n=[mt_n 'flag = i > 0 means test i rejected data.']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 89 |
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end; |
| 90 |
gforget |
1.12 |
% |
| 91 |
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list_interpr={'prof_interp_XC11','prof_interp_YC11','prof_interp_XCNINJ','prof_interp_YCNINJ'}; |
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for ii=1:length(list_interpr); |
| 93 |
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mt_v=[mt_v list_interpr{ii}]; mt_u=[mt_u 'unknown']; mt_n=[mt_n 'interpolation variable']; mt_d=[mt_d 'iPROF']; |
| 94 |
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end; |
| 95 |
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list_interpr={'prof_interp_i','prof_interp_j','prof_interp_lon','prof_interp_lat','prof_interp_weights'}; |
| 96 |
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for ii=1:length(list_interpr); |
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mt_v=[mt_v list_interpr{ii}]; mt_u=[mt_u 'unknown']; mt_n=[mt_n 'interpolation variable']; mt_d=[mt_d 'iPROF,iINTERP']; |
| 98 |
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end; |
| 99 |
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% |
| 100 |
gforget |
1.11 |
if 0; |
| 101 |
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mt_v=[mt_v 'prof_U']; mt_u=[mt_u 'm/s']; mt_n=[mt_n 'eastward velocity comp.']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 102 |
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mt_v=[mt_v 'prof_Uweight']; mt_u=[mt_u '(m/s)^-2']; mt_n=[mt_n 'east. v. least-square weight']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 103 |
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mt_v=[mt_v 'prof_V']; mt_u=[mt_u 'm/s']; mt_n=[mt_n 'northward velocity comp.']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 104 |
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mt_v=[mt_v 'prof_Vweight']; mt_u=[mt_u '(m/s)^-2']; mt_n=[mt_n 'north. v. least-square weight']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 105 |
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mt_v=[mt_v 'prof_ptr']; mt_u=[mt_u 'X']; mt_n=[mt_n 'passive tracer']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 106 |
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mt_v=[mt_v 'prof_ptrweight']; mt_u=[mt_u '(X)^-2']; mt_n=[mt_n 'pass. tracer least-square weight']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 107 |
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% |
| 108 |
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mt_v=[mt_v 'prof_D']; mt_u=[mt_u 'me']; mt_n=[mt_n 'variable depth']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 109 |
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mt_v=[mt_v 'prof_Destim']; mt_u=[mt_u 'me']; mt_n=[mt_n 'variable depth estimate (e.g. from atlas)']; mt_d=[mt_d 'iPROF,iDEPTH']; |
| 110 |
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% |
| 111 |
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mt_v=[mt_v 'prof_bp']; mt_u=[mt_u 'cm']; mt_n=[mt_n 'bottom pressure']; mt_d=[mt_d 'iPROF']; |
| 112 |
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mt_v=[mt_v 'prof_bpweight']; mt_u=[mt_u '(cm)^-2']; mt_n=[mt_n 'bot. pres. least-square weight']; mt_d=[mt_d 'iPROF']; |
| 113 |
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mt_v=[mt_v 'prof_ssh']; mt_u=[mt_u 'cm']; mt_n=[mt_n 'sea surface height']; mt_d=[mt_d 'iPROF']; |
| 114 |
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mt_v=[mt_v 'prof_sshweight']; mt_u=[mt_u '(cm)^-2']; mt_n=[mt_n 'ssh least-square weight']; mt_d=[mt_d 'iPROF']; |
| 115 |
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end; |
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gforget |
1.1 |
|
| 117 |
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%=============================create the file=================================% |
| 118 |
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| 119 |
roquet |
1.6 |
% write the netcdf structure |
| 120 |
roquet |
1.7 |
ncid=nccreate(fileOut,'clobber'); |
| 121 |
roquet |
1.6 |
|
| 122 |
roquet |
1.7 |
aa=sprintf(['Format: MITprof netcdf. This file was created using \n' ... |
| 123 |
roquet |
1.6 |
'the matlab toolbox which can be obtained (see README) from \n'... |
| 124 |
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'http://mitgcm.org/viewvc/MITgcm/MITgcm_contrib/gael/profilesMatlabProcessing/']); |
| 125 |
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ncputAtt(ncid,'','description',aa); |
| 126 |
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ncputAtt(ncid,'','date',date); |
| 127 |
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| 128 |
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ncdefDim(ncid,'iPROF',iPROF); |
| 129 |
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ncdefDim(ncid,'iDEPTH',iDEPTH); |
| 130 |
gforget |
1.12 |
ncdefDim(ncid,'iINTERP',iINTERP); |
| 131 |
roquet |
1.6 |
ncdefDim(ncid,'lTXT',lTXT); |
| 132 |
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| 133 |
gforget |
1.11 |
for ii=1:length(list_vars); |
| 134 |
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jj=find(strcmp(mt_v,list_vars{ii})); |
| 135 |
roquet |
1.6 |
if ~isempty(jj); |
| 136 |
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if strcmp(mt_d{jj},'iPROF,iDEPTH'); |
| 137 |
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ncdefVar(ncid,mt_v{jj},'double',{'iDEPTH','iPROF'});%note the direction flip |
| 138 |
gforget |
1.12 |
elseif strcmp(mt_d{jj},'iPROF,iINTERP'); |
| 139 |
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ncdefVar(ncid,mt_v{jj},'double',{'iINTERP','iPROF'});%note the direction flip |
| 140 |
gforget |
1.5 |
else; |
| 141 |
roquet |
1.6 |
ncdefVar(ncid,mt_v{jj},'double',{mt_d{jj}}); |
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gforget |
1.5 |
end; |
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roquet |
1.6 |
ncputAtt(ncid,mt_v{jj},'long_name',mt_n{jj}); |
| 144 |
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ncputAtt(ncid,mt_v{jj},'units',mt_u{jj}); |
| 145 |
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ncputAtt(ncid,mt_v{jj},'missing_value',fillval); |
| 146 |
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ncputAtt(ncid,mt_v{jj},'_FillValue',fillval); |
| 147 |
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else; |
| 148 |
gforget |
1.11 |
if strcmp(list_vars{ii},'prof_descr') |
| 149 |
roquet |
1.8 |
ncdefVar(ncid,'prof_descr','char',{'lTXT','iPROF'}); |
| 150 |
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ncputAtt(ncid,'prof_descr','long_name','profile description'); |
| 151 |
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else |
| 152 |
gforget |
1.11 |
warning([list_vars{ii} ' not included -- it is not a MITprof variable']); |
| 153 |
roquet |
1.8 |
end |
| 154 |
gforget |
1.1 |
end; |
| 155 |
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end; |
| 156 |
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| 157 |
roquet |
1.6 |
ncclose(ncid); |
| 158 |
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| 159 |
roquet |
1.7 |
%=============================set prof_depth=================================% |
| 160 |
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| 161 |
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ncid=ncopen(fileOut,'write'); |
| 162 |
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ncputvar(ncid,'prof_depth',prof_depth); |
| 163 |
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ncclose(ncid); |
| 164 |
gforget |
1.5 |
|
| 165 |
gforget |
1.1 |
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