update directory and file handling

- By default: dir_model is where MITgcm directory where *.nc MITgcm
input files and profiles/*bin MITgcm output files are.
- Remove '*' or '.nc' from file names if included.
- Update list_model default and help section accordingly.

MITprof_IO/MITprof_gcm2nc.m

@@ -1,29 +1,32 @@
 function []=MITprof_gcm2nc(varargin);
-%[]=MITprof_gcm2nc;
-%[]=MITprof_gcm2nc;
-%object:	takes binary output from MITgcm/pkg/profiles (in dir_model)
-%		and recomposes a MITprof netcdf file (in dir_model/input)
-%optional inputs:
-%		dir_model is the directory where the binary files are ('./' by default)
-%		list_model is the list of the corresponding MITprof files, which 
-%		need to be copied or linked to dir_model/input
-%		({'seals*','WOD09_XBT*','WOD09_CTD*','argo_at*','argo_pa*','argo_in*'} by default)
+%MITPROF_GCM2NC(dir_model,list_model);
 %
-%e.g.		dir_model='./';
-%		list_model={'seals*','WOD09_XBT*','WOD09_CTD*','argo_at*','argo_pa*','argo_in*'};
+%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);
-%note:
-%		by assumption, dir_model contains the binaries,
-%		dir_model/input contains the matching MITprof file
-%		that was provided as input to MITgcm/pkg/profiles, and
-%		the recomposed MITprof file will be put in dir_model/output
 
 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={'seals*','WOD09_XBT*','WOD09_CTD*','argo_at*','argo_pa*','argo_in*'};
+  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);
@@ -35,18 +38,23 @@
   dir_model=[dir_model{1} 'profiles/'];
 else;
   %the following assumes that
-  %dir_model is where MITgcm input and output files have been linked to dir_model (*.bin)
-  %and dir_model/input/ (*.nc) -- the new *.nc files will then be created in dir_model/output/
-  dir_out=[dir_model 'output/'];
-  dir_data=[dir_model 'input/'];
+  %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 list_model{ff}  '*.nc']);
+    file_data=dir([dir_data fil_root '*.nc']);
     file_data2=file_data.name;
 
     %load the data:
@@ -66,7 +74,7 @@
     nr=length(MITprof.prof_depth);
 
     %list tile/processor model files:
-    eval(['model_list_model=dir(''' dir_model list_model{ff} '*.data'');']);
+    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']);