changes to use matlab native netcdf

 Committer: PStar User Account <pstar@192.168.122.1>

 On branch dy113
 Changes to be committed:

	modified:   source/msubs/m_add_variable_name.m
	modified:   source/msubs/m_read_header.m
	modified:   source/msubs/m_unpack_dimnames.m
	modified:   source/msubs/m_unpack_varnames.m
	modified:   source/msubs/m_write_variable.m
	modified:   source/unfinished/m_ismstar.m

source/msubs/m_add_variable_name.m

@@ -18,7 +18,26 @@ if nargin < 3
 end
 
 
-metadata = nc_infoqdim(ncfile.name); %refresh metadata
+if exist('ncinfo','file') == 2 % jc191 use matlab netcdf if available
+    % make metadata look the same as the old snctools nc_info
+    % dm is the matlab data structure; dr is the reconstructed one.
+    clear dm dr
+    dm = ncinfo(ncfile.name);
+    
+    dr.Filename = ncfile.name;
+    dr.Attribute = dm.Attributes; % don't need in add_variable_name
+    dr.Dimension = dm.Dimensions(:);
+    for kl = 1:length(dm.Variables);
+        dr.Dataset(kl).Name = dm.Variables(kl).Name;
+        dr.Dataset(kl).Dimension = dm.Variables(kl).Dimensions.Name;
+        dr.Dataset(kl).Nctype = find(strcmp(dm.Variables(kl).Datatype,{'' 'char' '' '' '' 'double' ''}));
+    end
+    if isfield(dr,'Dataset'); dr.Dataset = dr.Dataset(:); end
+    metadata = dr;
+else
+    metadata = nc_infoqdim(ncfile.name); %refresh metadata % command before jc191
+end
+
 ncfile.metadata = metadata;
 
 dimnames = m_unpack_dimnames(ncfile);

source/msubs/m_read_header.m

@@ -11,7 +11,27 @@ ncfile = m_resolve_filename(ncfile);
 
 ncfile = m_ismstar(ncfile); % check it is an mstar file
 
-metadata = nc_infoqatt(ncfile.name); %refresh metadata
+if exist('ncinfo','file') == 2 % jc191 use matlab netcdf if available
+    % make metadata look the same as the old snctools nc_info
+    % dm is the matlab data structure; dr is the reconstructed one.
+    clear dm dr
+    dm = ncinfo(ncfile.name);
+    
+    dr.Filename = ncfile.name;
+    dr.Attribute = dm.Attributes; % don't need in add_variable_name
+    dr.Dimension = dm.Dimensions(:);
+    for kl = 1:length(dm.Variables);
+        dr.Dataset(kl).Name = dm.Variables(kl).Name;
+        dr.Dataset(kl).Dimension = dm.Variables(kl).Dimensions.Name;
+        dr.Dataset(kl).Nctype = find(strcmp(dm.Variables(kl).Datatype,{'' 'char' '' '' '' 'double' ''}));
+    end
+    if isfield(dr,'Dataset'); dr.Dataset = dr.Dataset(:); end
+    metadata = dr;
+else
+    metadata = nc_infoqatt(ncfile.name); %refresh metadata % command before jc191
+end
+
+
 ncfile.metadata = metadata;
 var_names = m_unpack_varnames(ncfile);
 dimnames = m_unpack_dimnames(ncfile);

source/msubs/m_unpack_dimnames.m

@@ -6,7 +6,25 @@ function dim_names = m_unpack_dimnames(ncfile)
 % If the metadata isn't in the structure ncfile, then read it from the file
 
 if ~isfield(ncfile,'metadata')
-    metadata = nc_info(ncfile.name);
+    if exist('ncinfo','file') == 2 % jc191 use matlab netcdf if available
+        % make metadata look the same as the old snctools nc_info
+        % dm is the matlab data structure; dr is the reconstructed one.
+        clear dm dr
+        dm = ncinfo(ncfile.name);
+        
+        dr.Filename = ncfile.name;
+        dr.Attribute = dm.Attributes; % don't need in add_variable_name
+        dr.Dimension = dm.Dimensions(:);
+        for kl = 1:length(dm.Variables);
+            dr.Dataset(kl).Name = dm.Variables(kl).Name;
+            dr.Dataset(kl).Dimension = dm.Variables(kl).Dimensions.Name;
+            dr.Dataset(kl).Nctype = find(strcmp(dm.Variables(kl).Datatype,{'' 'char' '' '' '' 'double' ''}));
+        end
+        if isfield(dr,'Dataset'); dr.Dataset = dr.Dataset(:); end
+        metadata = dr;
+    else
+        metadata = nc_info(ncfile.name); % command before jc191
+    end
     ncfile.metadata = metadata;
 end
 

source/msubs/m_unpack_varnames.m

@@ -3,36 +3,63 @@ function var_names = m_unpack_varnames(ncfile)
 % Unpack variable names from netcdf file
 
 %If the metadata isn't passed in, then read it from the file
-ncfile.name
-[ncid,MEXEC.status] = mexnc('open',ncfile.name,nc_nowrite_mode);
-[ndims, nvars, ngatts, record_dimension, MEXEC.status] = mexnc('INQ', ncid);
-
-var_names = cell(nvars,1);
-
-for k = 1:nvars; 
-    [varname, datatype, ndims, dims, natts, MEXEC.status] = mexnc('INQ_VAR', ncid, k-1); 
-    var_names{k} = varname;
-end;
-
-MEXEC.status = mexnc('close',ncid);
-
-% % if ~isfield(ncfile,'metadata')
-% %     metadata = nc_info(ncfile.name);
-% %     ncfile.metadata = metadata;
-% % end
-% % 
-% % metadata = ncfile.metadata;
-% % 
-% % if isfield ( metadata, 'Dataset' )
-% %     num_vars = length(metadata.Dataset);
-% % else
-% %     num_vars = 0;
-% % end
-% % 
-% % var_names = cell(num_vars,1);
-% % 
-% % for k = 1:num_vars
-% %     var_names{k} =  metadata.Dataset(k).Name;
-% % end
-% % 
-% % return
\ No newline at end of file
+
+% % % % % % the version at the start of jc191 had been written to make
+% direct call to mexnc, but I'm not sure why. There seems no reason to
+% force the read of metadata if it has already been read.
+% % % % % 
+% % % % % [ncid,MEXEC.status] = mexnc('open',ncfile.name,nc_nowrite_mode);
+% % % % % [ndims, nvars, ngatts, record_dimension, MEXEC.status] = mexnc('INQ', ncid);
+% % % % % 
+% % % % % var_names = cell(nvars,1);
+% % % % % 
+% % % % % for k = 1:nvars; 
+% % % % %     [varname, datatype, ndims, dims, natts, MEXEC.status] = mexnc('INQ_VAR', ncid, k-1); 
+% % % % %     var_names{k} = varname;
+% % % % % end;
+% % % % % 
+% % % % % MEXEC.status = mexnc('close',ncid);
+
+% jc191 reinstate previous logic, with faster call if varnames need to be
+% read in. 
+
+% often, metadata will be passed in and does not need to be read again
+
+if ~isfield(ncfile,'metadata')
+    if exist('ncinfo','file') == 2 % jc191 use matlab netcdf if available
+        % make metadata look the same as the old snctools nc_info
+        % dm is the matlab data structure; dr is the reconstructed one.
+        clear dm dr
+        dm = ncinfo(ncfile.name);
+        
+        dr.Filename = ncfile.name;
+        dr.Attribute = dm.Attributes; % don't need in add_variable_name
+        dr.Dimension = dm.Dimensions(:);
+        for kl = 1:length(dm.Variables);
+            dr.Dataset(kl).Name = dm.Variables(kl).Name;
+            dr.Dataset(kl).Dimension = dm.Variables(kl).Dimensions.Name;
+            dr.Dataset(kl).Nctype = find(strcmp(dm.Variables(kl).Datatype,{'' 'char' '' '' '' 'double' ''}));
+        end
+        if isfield(dr,'Dataset'); dr.Dataset = dr.Dataset(:); end
+        metadata = dr;
+    else
+        metadata = nc_info(ncfile.name); % command before jc191
+    end
+    ncfile.metadata = metadata;
+end
+
+metadata = ncfile.metadata;
+
+if isfield ( metadata, 'Dataset' )
+    num_vars = length(metadata.Dataset);
+else
+    num_vars = 0;
+end
+
+var_names = cell(num_vars,1);
+
+for k = 1:num_vars
+    var_names{k} =  metadata.Dataset(k).Name;
+end
+
+return
\ No newline at end of file

source/msubs/m_write_variable.m

@@ -26,7 +26,25 @@ end
 d1 = s(1);
 d2 = s(2);
 
-metadata = nc_infoqdim(ncfile.name); %refresh metadata
+if exist('ncinfo','file') == 2 % jc191 use matlab netcdf if available
+    % make metadata look the same as the old snctools nc_info
+    % dm is the matlab data structure; dr is the reconstructed one.
+    clear dm dr
+    dm = ncinfo(ncfile.name);
+    
+    dr.Filename = ncfile.name;
+    dr.Attribute = dm.Attributes; % don't need in add_variable_name
+    dr.Dimension = dm.Dimensions(:);
+    for kl = 1:length(dm.Variables);
+        dr.Dataset(kl).Name = dm.Variables(kl).Name;
+        dr.Dataset(kl).Dimension = dm.Variables(kl).Dimensions.Name;
+        dr.Dataset(kl).Nctype = find(strcmp(dm.Variables(kl).Datatype,{'' 'char' '' '' '' 'double' ''}));
+    end
+    if isfield(dr,'Dataset'); dr.Dataset = dr.Dataset(:); end
+    metadata = dr;
+else
+    metadata = nc_infoqdim(ncfile.name); %refresh metadata % command before jc191
+end
 ncfile.metadata = metadata;
 
 dimnames = m_unpack_dimnames(ncfile);

source/unfinished/m_ismstar.m

-function ncfile = m_ismstar(ncfile,opt)
-% function ncfile = m_ismstar(ncfile,opt)
+function ncfile = m_ismstar(ncfile)
+% function ncfile = m_ismstar(ncfile)
 %
 % Check if a file is an mstar NetCDF file
+% v4 version by bak on jc191; Use matlab native netcdf;
+% bak jc191 removed second argument 'opt' which was never used
 
 if nargin ~= 1
     error('Must supply precisely one argument to m_ismstar');
@@ -9,6 +11,35 @@ end
 
 ncfile.name = m_add_nc(ncfile.name);
 
+% bak will this become v4, using matlab netcdf commands ? jc191: use a single try and matlab native netcdf to try to check
+% for a mstar netcdf file
+
+if exist('ncreadatt','file') == 2 % ncreadatt.m is an available command
+    try
+        s = ncreadatt(ncfile.name,'/','mstar_string');
+    catch 
+        if exist(ncfile.name,'file') ~= 2
+            errstr0 = sprintf('\n%s',['The file ' ncfile.name ' does not exist']);
+            error(errstr0);
+        else
+            errstr0 = sprintf('\n%s',['The file ' ncfile.name ' exists but does not contain the mstar_string']);
+            error(errstr0);
+        end
+    end
+    if ~strcmp(s(1:5),'mstar')
+        errstr0 = sprintf('\n%s',['The file ' ncfile.name ' exists but the mstar_string contents are wrong']);
+        error(errstr0);
+    end
+    return
+end
+
+% bak jc191: old code follows here and should function as before if
+% ncreadatt doesnt exist.
+% if the matlab netcdf command readatt exists, then the code will have
+% exited before this point, either with the catch case, or after
+% successfully determining that it is an OK mstar file. If ncreadatt
+% is not available, then we revert to the old snctools code of nc_info.
+
 %check file exists
 if exist(ncfile.name,'file') ~= 2
     error(['Checking existence of mstar file: Filename ''' ncfile.name ''' not found']);