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gforget |
1.3 |
function []=MITprof_gcm2nc(varargin); |
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%[]=MITprof_gcm2nc; |
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%[]=MITprof_gcm2nc; |
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%object: takes binary output from MITgcm/pkg/profiles (in dir_model) |
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% and recomposes a MITprof netcdf file (in dir_model/input) |
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%optional inputs: |
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% dir_model is the directory where the binary files are ('./' by default) |
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% list_model is the list of the corresponding MITprof files, which |
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% need to be copied or linked to dir_model/input |
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% ({'seals*','WOD09_XBT*','WOD09_CTD*','argo_at*','argo_pa*','argo_in*'} by default) |
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% |
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%e.g. dir_model='./'; |
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% list_model={'seals*','WOD09_XBT*','WOD09_CTD*','argo_at*','argo_pa*','argo_in*'}; |
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gforget |
1.1 |
% MITprof_gcm2nc(dir_model,list_model); |
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%note: |
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% by assumption, dir_model contains the binaries, |
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% dir_model/input contains the matching MITprof file |
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roquet |
1.2 |
% that was provided as input to MITgcm/pkg/profiles, and |
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gforget |
1.1 |
% the recomposed MITprof file will be put in dir_model/output |
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warning off MATLAB:mir_warning_variable_used_as_function; |
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gforget |
1.4 |
if nargin==2; dir_model=varargin{1}; list_model=varargin{2}; |
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gforget |
1.3 |
else; |
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dir_model='./'; |
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list_model={'seals*','WOD09_XBT*','WOD09_CTD*','argo_at*','argo_pa*','argo_in*'}; |
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end; |
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gforget |
1.8 |
if iscell(dir_model); |
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%the following assumes that |
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%dir_model{1} is the run directory where *.nc MITgcm input files and profiles/*bin MITgcm output files are |
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%dir_model{2} typically is dirMat/profiles/output/ and is where the new *.nc files will be created |
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dir_out=dir_model{2}; |
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dir_data=dir_model{1}; |
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dir_model=[dir_model{1} 'profiles/']; |
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else; |
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%the following assumes that |
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%dir_model is where MITgcm input and output files have been linked to dir_model (*.bin) |
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%and dir_model/input/ (*.nc) -- the new *.nc files will then be created in dir_model/output/ |
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dir_out=[dir_model 'output/']; |
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dir_data=[dir_model 'input/']; |
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end; |
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gforget |
1.1 |
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%loop over files: |
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for ff=1:length(list_model) |
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roquet |
1.2 |
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%initialize the process: |
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clear prof_*; |
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file_data=dir([dir_data list_model{ff} '*.nc']); |
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file_data2=file_data.name; |
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%load the data: |
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MITprof=MITprof_load([dir_data file_data2]); |
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%prepare relevant output: |
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gforget |
1.5 |
varList={'T','S','U','V','ptr','ssh','OXY'}; |
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varMax=length(varList); |
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gforget |
1.6 |
varNum=zeros(varMax,1); varCount=0; |
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gforget |
1.5 |
for v=1:varMax; vv=varList{v}; |
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roquet |
1.2 |
if isfield(MITprof,['prof_' vv]); |
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varCount=varCount+1; varNum(v)=varCount; |
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eval(['prof_' vv '=-9999*ones(size(MITprof.prof_' vv ')); prof_' vv 'mask=prof_' vv ';']); |
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end; |
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end; |
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varList={varList{find(varNum)}}; |
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nr=length(MITprof.prof_depth); |
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%list tile/processor model files: |
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eval(['model_list_model=dir(''' dir_model list_model{ff} '*.data'');']); |
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%if no model files then stop |
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if size(model_list_model,1)==0; fprintf(['file: ' file_data2 ' \n, no model files found\n']); |
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else; |
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%loop over model files: |
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for ffM=1:length(model_list_model) |
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file_model2=model_list_model(ffM).name; |
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np=model_list_model(ffM).bytes/8/2/(nr+1)/varCount; |
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tmp_prof=read2memory([dir_model file_model2],[nr+1 2 varCount np],64); |
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for v=1:varCount; vv=varList{v}; |
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tmp1=squeeze(tmp_prof(1:nr,1,v,:))'; tmp2=squeeze(tmp_prof(1:nr,2,v,:))'; tmp3=squeeze(tmp_prof(nr+1,1,v,:)); |
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tmp4=find(tmp3>0); tmp1=tmp1(tmp4,:); tmp2=tmp2(tmp4,:); tmp3=tmp3(tmp4,:); |
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eval(['prof_' vv '(tmp3,:)=tmp1; prof_' vv 'mask(tmp3,:)=tmp2;']); |
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end; |
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end; %for ffM |
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%include in structure: |
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for v=1:varCount; vv=varList{v}; eval(['prof_' vv '(prof_' vv 'mask==0)=-9999; MITprof.prof_' vv 'estim=prof_' vv ';']); end; |
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%prepare fields list: |
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list_out=fieldnames(MITprof)'; |
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ii=find(strncmp(list_out,'prof_U',6)+strncmp(list_out,'prof_S',6)+strncmp(list_out,'prof_T',6)+... |
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gforget |
1.5 |
strncmp(list_out,'prof_V',6)+strncmp(list_out,'prof_ssh',8)+strncmp(list_out,'prof_ptr',8)+... |
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strncmp(list_out,'prof_OXY',8)); |
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roquet |
1.2 |
list_out={list_out{ii}}; |
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%prepare other fields: |
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file_out=[file_data2(1:end-3) '_model.nc']; |
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nr=length(MITprof.prof_depth); |
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np=length(MITprof.prof_lon); |
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%write to file: |
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gforget |
1.7 |
fprintf(['writing file: ' file_data2 ' \n']); |
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roquet |
1.2 |
MITprof_write([dir_out file_out],MITprof); |
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fprintf(['file: ' file_data2 ' \n has been processed \n']); |
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end %if size(model_list_model,1)~=0; |
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gforget |
1.1 |
end%for ff=1:length(list_model) |
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