profilesMatlabProcessing/profiles_IO_v2/MITprof_gcm2nc.m

function []=MITprof_gcm2nc(varargin);
%MITPROF_GCM2NC(dir_model,list_model);
%
%object:        reformat MITprof binary files from MITgcm into MITprof netcdf files
%
%inputs:
%               dir_model is the directory where the binary files are ('./' by default). If dir_model is a cell containing 
%                 two directory names then the first will be used for inputs whereas the second will be used for output.
%                 By assumption the input directory contains the nc files listed in list_model and a subdirectory called
%                 'profiles/' that contains the corresponding binary files generated by MITgcm
%               list_model is the list of the corresponding MITprof files; by default:
%                  {'argo_feb2016_set1.nc','argo_feb2016_set2.nc','argo_feb2016_set3.nc','argo_feb2016_set4.nc','argo_feb2016_set5.nc',...
%                   'argo_feb2016_set6.nc','climode_jan2016.nc','ctd_jan2016.nc','itp_jan2016.nc','seals_jan2016.nc','xbt_jan2016.nc'}
%
%example:
%               MITprof_gcm2nc;
%or:
%               dir_model='./';
%               list_model={'argo_feb2016_set1.nc','argo_feb2016_set2.nc','argo_feb2016_set3.nc','argo_feb2016_set4.nc','argo_feb2016_set5.nc',...
%                           'argo_feb2016_set6.nc','climode_jan2016.nc','ctd_jan2016.nc','itp_jan2016.nc','seals_jan2016.nc','xbt_jan2016.nc'};
%               MITprof_gcm2nc(dir_model,list_model);

warning off MATLAB:mir_warning_variable_used_as_function;

if nargin==2; dir_model=varargin{1}; list_model=varargin{2}; 
else; 
  dir_model='./'; 
  list_model={'argo_feb2016_set1.nc','argo_feb2016_set2.nc','argo_feb2016_set3.nc','argo_feb2016_set4.nc','argo_feb2016_set5.nc',...
              'argo_feb2016_set6.nc','climode_jan2016.nc','ctd_jan2016.nc','itp_jan2016.nc','seals_jan2016.nc','xbt_jan2016.nc'};
end;

if iscell(dir_model);
  %the following assumes that
  %dir_model{1} is the run directory where *.nc MITgcm input files and profiles/*bin MITgcm output files are
  %dir_model{2} typically is dirMat/profiles/output/ and is where the new *.nc files will be created
  dir_out=dir_model{2};
  dir_data=dir_model{1};
  dir_model=[dir_model{1} 'profiles/'];
else;
  %the following assumes that
  %dir_model is where MITgcm directory where *.nc MITgcm input files and profiles/*bin MITgcm output files are
  %and where the new *model.nc files will then be created
  dir_out=dir_model;
  dir_data=dir_model;
  dir_model=[dir_model 'profiles/'];
end;

%loop over files:
for ff=1:length(list_model)

    fil_root=list_model{ff};
    if strcmp(fil_root(end-2:end),'.nc'); fil_root=fil_root(1:end-3); end;
    if strcmp(fil_root(end),'*'); fil_root=fil_root(1:end-1); end;
    
    %initialize the process:
    clear prof_*;
    file_data=dir([dir_data fil_root '*.nc']);
    file_data2=file_data.name;
    
    %load the data:
    MITprof=MITprof_load([dir_data file_data2]);
    
    %prepare relevant output:
    varList={'T','S','U','V','ptr','ssh','OXY'};
    varMax=length(varList);
    varNum=zeros(varMax,1); varCount=0;
    for v=1:varMax; vv=varList{v};
        if isfield(MITprof,['prof_' vv]);
            varCount=varCount+1; varNum(v)=varCount;
            eval(['prof_' vv '=-9999*ones(size(MITprof.prof_' vv ')); prof_' vv 'mask=prof_' vv ';']);
        end;
    end;
    varList={varList{find(varNum)}};
    nr=length(MITprof.prof_depth);
    
    %list tile/processor model files:
    eval(['model_list_model=dir(''' dir_model fil_root '*.data'');']);
    
    %if no model files then stop
    if size(model_list_model,1)==0; fprintf(['file: ' file_data2 ' \n, no model files found\n']);
    else;
        
        %loop over model files:
        for ffM=1:length(model_list_model)
            file_model2=model_list_model(ffM).name;
            np=model_list_model(ffM).bytes/8/2/(nr+1)/varCount;
            tmp_prof=read2memory([dir_model file_model2],[nr+1 2 varCount np],64);
            
            for v=1:varCount; vv=varList{v};
                tmp1=squeeze(tmp_prof(1:nr,1,v,:))'; tmp2=squeeze(tmp_prof(1:nr,2,v,:))'; tmp3=squeeze(tmp_prof(nr+1,1,v,:));
                tmp4=find(tmp3>0); tmp1=tmp1(tmp4,:); tmp2=tmp2(tmp4,:); tmp3=tmp3(tmp4,:);
                eval(['prof_' vv '(tmp3,:)=tmp1; prof_' vv 'mask(tmp3,:)=tmp2;']);
            end;
        end; %for ffM
        
        %include in structure:
        for v=1:varCount; vv=varList{v}; eval(['prof_' vv '(prof_' vv 'mask==0)=-9999; MITprof.prof_' vv 'estim=prof_' vv ';']); end;
        
        %prepare fields list:
        list_out=fieldnames(MITprof)';
        ii=find(strncmp(list_out,'prof_U',6)+strncmp(list_out,'prof_S',6)+strncmp(list_out,'prof_T',6)+...
            strncmp(list_out,'prof_V',6)+strncmp(list_out,'prof_ssh',8)+strncmp(list_out,'prof_ptr',8)+...
            strncmp(list_out,'prof_OXY',8));
        list_out={list_out{ii}};
        %prepare other fields:
        file_out=[file_data2(1:end-3) '_model.nc'];
        nr=length(MITprof.prof_depth);
        np=length(MITprof.prof_lon);
        %write to file:
        fprintf(['writing file: ' file_data2 ' \n']);
        MITprof_write([dir_out file_out],MITprof);
        
        fprintf(['file: ' file_data2 ' \n has been processed \n']);
    end %if size(model_list_model,1)~=0;
end%for ff=1:length(list_model)


1	gforget	1.3	function []=MITprof_gcm2nc(varargin);
2	gforget	1.9	%MITPROF_GCM2NC(dir_model,list_model);
3	gforget	1.3	%
4	gforget	1.9	%object: reformat MITprof binary files from MITgcm into MITprof netcdf files
5			%
6			%inputs:
7			% dir_model is the directory where the binary files are ('./' by default). If dir_model is a cell containing
8			% two directory names then the first will be used for inputs whereas the second will be used for output.
9			% By assumption the input directory contains the nc files listed in list_model and a subdirectory called
10			% 'profiles/' that contains the corresponding binary files generated by MITgcm
11			% list_model is the list of the corresponding MITprof files; by default:
12			% {'argo_feb2016_set1.nc','argo_feb2016_set2.nc','argo_feb2016_set3.nc','argo_feb2016_set4.nc','argo_feb2016_set5.nc',...
13			% 'argo_feb2016_set6.nc','climode_jan2016.nc','ctd_jan2016.nc','itp_jan2016.nc','seals_jan2016.nc','xbt_jan2016.nc'}
14			%
15			%example:
16			% MITprof_gcm2nc;
17			%or:
18			% dir_model='./';
19			% list_model={'argo_feb2016_set1.nc','argo_feb2016_set2.nc','argo_feb2016_set3.nc','argo_feb2016_set4.nc','argo_feb2016_set5.nc',...
20			% 'argo_feb2016_set6.nc','climode_jan2016.nc','ctd_jan2016.nc','itp_jan2016.nc','seals_jan2016.nc','xbt_jan2016.nc'};
21	gforget	1.1	% MITprof_gcm2nc(dir_model,list_model);
22
23			warning off MATLAB:mir_warning_variable_used_as_function;
24
25	gforget	1.4	if nargin==2; dir_model=varargin{1}; list_model=varargin{2};
26	gforget	1.3	else;
27			dir_model='./';
28	gforget	1.9	list_model={'argo_feb2016_set1.nc','argo_feb2016_set2.nc','argo_feb2016_set3.nc','argo_feb2016_set4.nc','argo_feb2016_set5.nc',...
29			'argo_feb2016_set6.nc','climode_jan2016.nc','ctd_jan2016.nc','itp_jan2016.nc','seals_jan2016.nc','xbt_jan2016.nc'};
30	gforget	1.3	end;
31
32	gforget	1.8	if iscell(dir_model);
33			%the following assumes that
34			%dir_model{1} is the run directory where .nc MITgcm input files and profiles/bin MITgcm output files are
35			%dir_model{2} typically is dirMat/profiles/output/ and is where the new *.nc files will be created
36			dir_out=dir_model{2};
37			dir_data=dir_model{1};
38			dir_model=[dir_model{1} 'profiles/'];
39			else;
40			%the following assumes that
41	gforget	1.9	%dir_model is where MITgcm directory where .nc MITgcm input files and profiles/bin MITgcm output files are
42			%and where the new *model.nc files will then be created
43			dir_out=dir_model;
44			dir_data=dir_model;
45			dir_model=[dir_model 'profiles/'];
46	gforget	1.8	end;
47	gforget	1.1
48			%loop over files:
49			for ff=1:length(list_model)
50	gforget	1.9
51			fil_root=list_model{ff};
52			if strcmp(fil_root(end-2:end),'.nc'); fil_root=fil_root(1:end-3); end;
53			if strcmp(fil_root(end),'*'); fil_root=fil_root(1:end-1); end;
54	roquet	1.2
55			%initialize the process:
56			clear prof_*;
57	gforget	1.9	file_data=dir([dir_data fil_root '*.nc']);
58	roquet	1.2	file_data2=file_data.name;
59
60			%load the data:
61			MITprof=MITprof_load([dir_data file_data2]);
62
63			%prepare relevant output:
64	gforget	1.5	varList={'T','S','U','V','ptr','ssh','OXY'};
65			varMax=length(varList);
66	gforget	1.6	varNum=zeros(varMax,1); varCount=0;
67	gforget	1.5	for v=1:varMax; vv=varList{v};
68	roquet	1.2	if isfield(MITprof,['prof_' vv]);
69			varCount=varCount+1; varNum(v)=varCount;
70			eval(['prof_' vv '=-9999*ones(size(MITprof.prof_' vv ')); prof_' vv 'mask=prof_' vv ';']);
71			end;
72			end;
73			varList={varList{find(varNum)}};
74			nr=length(MITprof.prof_depth);
75
76			%list tile/processor model files:
77	gforget	1.9	eval(['model_list_model=dir(''' dir_model fil_root '*.data'');']);
78	roquet	1.2
79			%if no model files then stop
80			if size(model_list_model,1)==0; fprintf(['file: ' file_data2 ' \n, no model files found\n']);
81			else;
82
83			%loop over model files:
84			for ffM=1:length(model_list_model)
85			file_model2=model_list_model(ffM).name;
86			np=model_list_model(ffM).bytes/8/2/(nr+1)/varCount;
87			tmp_prof=read2memory([dir_model file_model2],[nr+1 2 varCount np],64);
88
89			for v=1:varCount; vv=varList{v};
90			tmp1=squeeze(tmp_prof(1:nr,1,v,:))'; tmp2=squeeze(tmp_prof(1:nr,2,v,:))'; tmp3=squeeze(tmp_prof(nr+1,1,v,:));
91			tmp4=find(tmp3>0); tmp1=tmp1(tmp4,:); tmp2=tmp2(tmp4,:); tmp3=tmp3(tmp4,:);
92			eval(['prof_' vv '(tmp3,:)=tmp1; prof_' vv 'mask(tmp3,:)=tmp2;']);
93			end;
94			end; %for ffM
95
96			%include in structure:
97			for v=1:varCount; vv=varList{v}; eval(['prof_' vv '(prof_' vv 'mask==0)=-9999; MITprof.prof_' vv 'estim=prof_' vv ';']); end;
98
99			%prepare fields list:
100			list_out=fieldnames(MITprof)';
101			ii=find(strncmp(list_out,'prof_U',6)+strncmp(list_out,'prof_S',6)+strncmp(list_out,'prof_T',6)+...
102	gforget	1.5	strncmp(list_out,'prof_V',6)+strncmp(list_out,'prof_ssh',8)+strncmp(list_out,'prof_ptr',8)+...
103			strncmp(list_out,'prof_OXY',8));
104	roquet	1.2	list_out={list_out{ii}};
105			%prepare other fields:
106			file_out=[file_data2(1:end-3) '_model.nc'];
107			nr=length(MITprof.prof_depth);
108			np=length(MITprof.prof_lon);
109			%write to file:
110	gforget	1.7	fprintf(['writing file: ' file_data2 ' \n']);
111	roquet	1.2	MITprof_write([dir_out file_out],MITprof);
112
113			fprintf(['file: ' file_data2 ' \n has been processed \n']);
114			end %if size(model_list_model,1)~=0;
115	gforget	1.1	end%for ff=1:length(list_model)
116
117