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function []=MITprof_gcm2nc(varargin); |
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%MITPROF_GCM2NC(dir_model,list_model); |
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% |
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%object: reformat MITprof binary files from MITgcm into MITprof netcdf files |
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% |
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%inputs: |
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% dir_model is the directory where the binary files are ('./' by default). If dir_model is a cell containing |
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% two directory names then the first will be used for inputs whereas the second will be used for output. |
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% By assumption the input directory contains the nc files listed in list_model and a subdirectory called |
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% 'profiles/' that contains the corresponding binary files generated by MITgcm |
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% list_model is the list of the corresponding MITprof files; by default: |
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% {'argo_feb2016_set1.nc','argo_feb2016_set2.nc','argo_feb2016_set3.nc','argo_feb2016_set4.nc','argo_feb2016_set5.nc',... |
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% 'argo_feb2016_set6.nc','climode_jan2016.nc','ctd_jan2016.nc','itp_jan2016.nc','seals_jan2016.nc','xbt_jan2016.nc'} |
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% |
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%example: |
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% MITprof_gcm2nc; |
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%or: |
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% dir_model='./'; |
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% list_model={'argo_feb2016_set1.nc','argo_feb2016_set2.nc','argo_feb2016_set3.nc','argo_feb2016_set4.nc','argo_feb2016_set5.nc',... |
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% 'argo_feb2016_set6.nc','climode_jan2016.nc','ctd_jan2016.nc','itp_jan2016.nc','seals_jan2016.nc','xbt_jan2016.nc'}; |
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% MITprof_gcm2nc(dir_model,list_model); |
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|
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warning off MATLAB:mir_warning_variable_used_as_function; |
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|
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if nargin==2; dir_model=varargin{1}; list_model=varargin{2}; |
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else; |
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dir_model='./'; |
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list_model={'argo_feb2016_set1.nc','argo_feb2016_set2.nc','argo_feb2016_set3.nc','argo_feb2016_set4.nc','argo_feb2016_set5.nc',... |
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'argo_feb2016_set6.nc','climode_jan2016.nc','ctd_jan2016.nc','itp_jan2016.nc','seals_jan2016.nc','xbt_jan2016.nc'}; |
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end; |
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|
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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 directory where *.nc MITgcm input files and profiles/*bin MITgcm output files are |
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%and where the new *model.nc files will then be created |
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dir_out=dir_model; |
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dir_data=dir_model; |
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dir_model=[dir_model 'profiles/']; |
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end; |
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|
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%loop over files: |
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for ff=1:length(list_model) |
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|
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fil_root=list_model{ff}; |
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if strcmp(fil_root(end-2:end),'.nc'); fil_root=fil_root(1:end-3); end; |
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if strcmp(fil_root(end),'*'); fil_root=fil_root(1:end-1); end; |
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|
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%initialize the process: |
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clear prof_*; |
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file_data=dir([dir_data fil_root '*.nc']); |
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file_data2=file_data.name; |
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|
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%load the data: |
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MITprof=MITprof_load([dir_data file_data2]); |
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|
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%prepare relevant output: |
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varList={'T','S','U','V','ptr','ssh','OXY'}; |
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varMax=length(varList); |
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varNum=zeros(varMax,1); varCount=0; |
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for v=1:varMax; vv=varList{v}; |
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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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|
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%list tile/processor model files: |
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eval(['model_list_model=dir(''' dir_model fil_root '*.data'');']); |
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|
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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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|
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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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|
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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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|
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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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|
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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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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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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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fprintf(['writing file: ' file_data2 ' \n']); |
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MITprof_write([dir_out file_out],MITprof); |
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|
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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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end%for ff=1:length(list_model) |
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