Changeset 1095 for trunk/src/nc2struct.m

Timestamp:

Mar 31, 2021, 3:32:03 PM (3 years ago)

Author:

sommeria

Message:

reading mat files added, +-fixed,OpenDAP improved

File:

• trunk/src/nc2struct.m (modified) (2 diffs)

trunk/src/nc2struct.m

@@ -1 +1 @@
 
 %'nc2struct': transform a NetCDF file in a corresponding matlab structure
+% or directly read the a matlab data file .mat (calling the fct mat2struct.m)
 % it reads all the global attributes and all variables, or a selected list.
 % The corresponding dimensions and variable attributes are then extracted
@@ -60 +61 @@
     varargin{1}='*';
 end
-hhh=which('netcdf.open');% look for built-in matlab NetCDF library
-
-if ~isempty(hhh)
-    %% default output
-    Data=[];%default
-    var_detect=[];%default
-    ichoice=[];%default
-
-    %% open the NetCDF file for reading
-    if ischar(nc)
-        if exist(nc,'file')
+
+%% default output
+Data=[];%default
+var_detect=[];%default
+ichoice=[];%default
+
+%% open the NetCDF (or .mat) file for reading
+if ischar(nc)
+    testfile=1;
+    if exist(nc,'file')
+        if ~isempty(regexp(nc,'.mat$'))
+            Data=mat2struct(nc,varargin{1});
+            return
+        else
             try
                 nc=netcdf.open(nc,'NC_NOWRITE');
-                testfile=1;
             catch ME
                 errormsg=['ERROR opening ' nc ': ' ME.message];
                 return
             end
+        end
+    else %case of OpenDAP files
+        if regexp(nc,'^http://')
+            try
+                nc=netcdf.open(nc,'NC_NOWRITE');
+            catch ME
+                errormsg=['ERROR opening ' nc ': ' ME.message];
+                return
+            end
         else
-            if regexp(nc,'^http://')
-                nc=netcdf.open(nc,'NC_NOWRITE');
-                testfile=1;
-            else
             errormsg=['ERROR:file ' nc ' does not exist'];
             return
-            end
-        end
+        end
+    end
+else
+    testfile=0;
+end
+
+%% short reading option for global attributes only, if the first argument is 'ListGlobalAttribute'
+if isequal(varargin{1},'ListGlobalAttribute')
+    for ilist=2:numel(varargin)
+        valuestr=[];%default
+        try
+            valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),varargin{ilist});
+        catch ME
+        end
+        eval(['Data.' varargin{ilist} '=valuestr;'])
+    end
+    netcdf.close(nc)
+    return
+end
+
+%% time variable or dimension
+input_index=1;
+CheckTimeVar=0;
+TimeVarName='';
+if isequal(varargin{1},'TimeVarName')
+    TimeVarName=varargin{2};
+    CheckTimeVar=1;
+    TimeIndex=varargin{3};
+    input_index=4;% list of variables to read is at fourth argument
+elseif isequal(varargin{1},'TimeDimName')
+    TimeDimName=varargin{2};
+    TimeIndex=varargin{3};
+    input_index=4;
+end
+
+%% full reading: get the nbre of dimensions, variables, global attributes
+ListVarName=varargin{input_index};
+[ndims,nvars,ngatts]=netcdf.inq(nc);%nbre of dimensions, variables, global attributes, in the NetCDF file
+
+%%  -------- read all global attributes (constants)-----------
+Data.ListGlobalAttribute={};%default
+att_key=cell(1,ngatts);%default
+for iatt=1:ngatts
+    keystr= netcdf.inqAttName(nc,netcdf.getConstant('NC_GLOBAL'),iatt-1);
+    valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),keystr);
+    keystr=regexprep(keystr,{'\','/','\.','-',' '},{'','','','',''});%remove  '\','.' or '-' if exists
+    if strcmp(keystr(1),'_')
+        keystr(1)=[];
+    end
+    try
+        if ischar(valuestr) %& length(valuestr)<200 & double(valuestr)<=122 & double(valuestr)>=48 %usual characters
+            eval(['Data.' keystr '=''' valuestr ''';'])
+        elseif isnumeric(valuestr)
+            eval(['Data.' keystr '=valuestr;'])
+        else
+            eval(['Data.' keystr '='';'])
+        end
+        att_key{iatt}=keystr;
+    catch ME
+        att_key{iatt}=['attr_' num2str(iatt)];
+        Data.(att_key{iatt})=[];
+    end
+end
+Data.ListGlobalAttribute=att_key;
+
+%%  -------- read dimension names-----------
+ListDimNameNetcdf=cell(1,ndims);
+dim_value=zeros(1,ndims);
+for idim=1:ndims %loop on the dimensions of the NetCDF file
+    [ListDimNameNetcdf{idim},dim_value(idim)] = netcdf.inqDim(nc,idim-1);%get name and value of each dimension
+end
+if ~isempty(ListDimNameNetcdf)
+    flag_used=zeros(1,ndims);%initialize the flag indicating the selected dimensions in the list (0=unused)
+end
+if isequal(varargin{1},'TimeDimName')% time dimension introduced
+    TimeDimIndex=find(strcmp(TimeDimName,ListDimNameNetcdf));
+    if isempty(TimeDimIndex)
+        errormsg=['requested time dimension ' varargin{2} ' not found'];
+        return
+    end
+    if dim_value(TimeDimIndex)<varargin{3}
+        errormsg=['requested time index ' num2str(varargin{3}) ' exceeds matrix dimension'];
+        return
+    end
+end
+
+%%  -------- read names of variables -----------
+ListVarNameNetcdf=cell(1,nvars); %default
+dimids=cell(1,nvars);
+nbatt=zeros(1,nvars);
+for ncvar=1:nvars %loop on the variables of the NetCDF file
+    %get name, type, dimensions and attribute numbers of each variable
+    [ListVarNameNetcdf{ncvar},xtype(ncvar),dimids{ncvar},nbatt(ncvar)] = netcdf.inqVar(nc,ncvar-1);
+end
+%     testmulti=0;
+if isequal(ListVarName,'*')||isempty(ListVarName)
+    var_index=1:nvars; %all the variables are selected in the NetCDF file
+    Data.ListVarName=ListVarNameNetcdf;
+else   %select input variables, if requested by the input ListVarName
+    check_keep=ones(1,size(ListVarName,2));
+    for ivar=1:size(ListVarName,2) % check redondancy of variable names
+        if ~isempty(find(strcmp(ListVarName{1,ivar},ListVarName(1:ivar-1)), 1))
+            check_keep(ivar)=0;% the variable #ivar is already in the list
+        end
+    end
+    ListVarName=ListVarName(:,logical(check_keep));
+    if size(ListVarName,1)>1 %multiple choice of variable ranked by order of priority
+        for iline=1:size(ListVarName,1)
+            search_index=find(strcmp(ListVarName{iline,1},ListVarNameNetcdf),1);%look for the first variable name in the list of NetCDF variables
+            if ~isempty(search_index)
+                break % go to the next line
+            end
+        end
+        ichoice=iline-1;%selected line number in the list of input names of variables
     else
-        testfile=0;
-    end
-
-    %% short reading option for global attributes only, if the first argument is 'ListGlobalAttribute'
-    if isequal(varargin{1},'ListGlobalAttribute')
-        for ilist=2:numel(varargin)
-            valuestr=[];%default
-            try
-                valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),varargin{ilist});
-            catch ME
-            end
-            eval(['Data.' varargin{ilist} '=valuestr;'])
-        end
-        netcdf.close(nc)
-        return
-    end
-
-    %% time variable or dimension
-    input_index=1;
-    CheckTimeVar=0;
-    TimeVarName='';
-    if isequal(varargin{1},'TimeVarName')
-        TimeVarName=varargin{2};
-        CheckTimeVar=1;
-        TimeIndex=varargin{3};
-        input_index=4;% list of variables to read is at fourth argument
-    elseif isequal(varargin{1},'TimeDimName')
-        TimeDimName=varargin{2};
-        TimeIndex=varargin{3};
-        input_index=4;
-    end
-
-    %% full reading: get the nbre of dimensions, variables, global attributes
-    ListVarName=varargin{input_index};
-    [ndims,nvars,ngatts]=netcdf.inq(nc);%nbre of dimensions, variables, global attributes, in the NetCDF file
-
-    %%  -------- read all global attributes (constants)-----------
-    Data.ListGlobalAttribute={};%default
-    att_key=cell(1,ngatts);%default
-    for iatt=1:ngatts
-        keystr= netcdf.inqAttName(nc,netcdf.getConstant('NC_GLOBAL'),iatt-1);
-        valuestr = netcdf.getAtt(nc,netcdf.getConstant('NC_GLOBAL'),keystr);
-        keystr=regexprep(keystr,{'\','/','\.','-',' '},{'','','','',''});%remove  '\','.' or '-' if exists
-        if strcmp(keystr(1),'_')
-            keystr(1)=[];
+        iline=1;
+    end
+    %ListVarName=ListVarName(iline,:);% select the appropriate option for input variable (lin ein the input name matrix)
+    if CheckTimeVar
+        TimeVarIndex=find(strcmp(TimeVarName,ListVarNameNetcdf),1); %look for the index of the time variable in the netcdf list
+        if isempty(TimeVarIndex)
+            errormsg='requested variable for time is missing';
+            return
+        end
+        TimeDimIndex=dimids{TimeVarIndex}(1)+1;
+        ListVarName=[ListVarName {TimeVarName}];
+    end
+    var_index=zeros(1,size(ListVarName,2));%default list of variable indices
+    for ivar=1:size(ListVarName,2)
+        search_index=find(strcmp(ListVarName{iline,ivar},ListVarNameNetcdf),1);%look for the variable name in the list of NetCDF file
+        if ~isempty(search_index)
+            var_index(ivar)=search_index;%index of the netcdf list corresponding to the input list index ivar
+        end
+    end
+    var_detect=(var_index~=0);%=1 for detected variables
+    list_index=find(var_index);% indices in the input list corresponding to a detected variable
+    var_index=var_index(list_index);% NetCDF variable indices corresponding to the output list of read variable
+    Data.ListVarName=ListVarName(1,list_index);%the first line of ListVarName sets the output names of the variables
+end
+
+%% get the dimensions and attributes associated to  variables
+var_dim=cell(size(var_index));% initiate list of dimensions for variables
+for ivar=1:length(var_index)
+    var_dim{ivar}=dimids{var_index(ivar)}+1; %netcdf dimension indices used by the variable #ivar
+    Data.VarDimName{ivar}=ListDimNameNetcdf(var_dim{ivar});
+    flag_used(var_dim{ivar})=ones(size(var_dim{ivar}));%flag_used =1 for the indices of used dimensions
+    for iatt=1:nbatt(var_index(ivar))
+        attname = netcdf.inqAttName(nc,var_index(ivar)-1,iatt-1);
+        valuestr= netcdf.getAtt(nc,var_index(ivar)-1,attname);
+        attname=regexprep(attname,{'\','/','\.','-',' '},{'','','','',''});%remove  '\','.' or '-' if exists
+        if strcmp(attname(1),'_')
+            attname(1)=[];
         end
         try
-            if ischar(valuestr) %& length(valuestr)<200 & double(valuestr)<=122 & double(valuestr)>=48 %usual characters
-                eval(['Data.' keystr '=''' valuestr ''';'])
-            elseif isnumeric(valuestr)
-                eval(['Data.' keystr '=valuestr;'])
-            else
-                eval(['Data.' keystr '='';'])
-            end
-            att_key{iatt}=keystr;
+            if ~isempty(valuestr)
+                Data.VarAttribute{ivar}.(attname)=valuestr;
+            end
         catch ME
-            att_key{iatt}=['attr_' num2str(iatt)];
-            Data.(att_key{iatt})=[];
-        end
-    end
-    Data.ListGlobalAttribute=att_key;
-
-    %%  -------- read dimension names-----------
-    ListDimNameNetcdf=cell(1,ndims);
-    dim_value=zeros(1,ndims);
-    for idim=1:ndims %loop on the dimensions of the NetCDF file
-        [ListDimNameNetcdf{idim},dim_value(idim)] = netcdf.inqDim(nc,idim-1);%get name and value of each dimension
-    end
-    if ~isempty(ListDimNameNetcdf)
-        flag_used=zeros(1,ndims);%initialize the flag indicating the selected dimensions in the list (0=unused)
-    end
-    if isequal(varargin{1},'TimeDimName')% time dimension introduced
-        TimeDimIndex=find(strcmp(TimeDimName,ListDimNameNetcdf));
-        if isempty(TimeDimIndex)
-            errormsg=['requested time dimension ' varargin{2} ' not found'];
-            return
-        end
-        if dim_value(TimeDimIndex)<varargin{3}
-           errormsg=['requested time index ' num2str(varargin{3}) ' exceeds matrix dimension'];
-            return
-        end
-    end
-
-    %%  -------- read names of variables -----------
-    ListVarNameNetcdf=cell(1,nvars); %default
-    dimids=cell(1,nvars);
-    nbatt=zeros(1,nvars);
-    for ncvar=1:nvars %loop on the variables of the NetCDF file
-        %get name, type, dimensions and attribute numbers of each variable
-        [ListVarNameNetcdf{ncvar},xtype(ncvar),dimids{ncvar},nbatt(ncvar)] = netcdf.inqVar(nc,ncvar-1);
-    end
-%     testmulti=0;
-    if isequal(ListVarName,'*')||isempty(ListVarName)
-        var_index=1:nvars; %all the variables are selected in the NetCDF file
-        Data.ListVarName=ListVarNameNetcdf;
-    else   %select input variables, if requested by the input ListVarName
-        check_keep=ones(1,size(ListVarName,2));
-        for ivar=1:size(ListVarName,2) % check redondancy of variable names
-            if ~isempty(find(strcmp(ListVarName{1,ivar},ListVarName(1:ivar-1)), 1))
-                check_keep(ivar)=0;% the variable #ivar is already in the list
-            end
-        end
-        ListVarName=ListVarName(:,logical(check_keep));
-        if size(ListVarName,1)>1 %multiple choice of variable ranked by order of priority
-            for iline=1:size(ListVarName,1)
-                search_index=find(strcmp(ListVarName{iline,1},ListVarNameNetcdf),1);%look for the first variable name in the list of NetCDF variables
-                if ~isempty(search_index)
-                    break % go to the next line
+            display(attname)
+            display(valuestr)
+            display(ME.message)
+            Data.VarAttribute{ivar}.(['atrr_' num2str(iatt)])='not read';
+        end
+    end
+end
+
+%% select the dimensions used for the set of input variables
+if ~isempty(var_index)
+    dim_index=find(flag_used);%list of netcdf dimensions indices corresponding to used dimensions
+    Data.ListDimName=ListDimNameNetcdf(dim_index);
+    Data.DimValue=dim_value(dim_index);
+    if input_index==4% if a dimension is selected as time
+        Data.DimValue(TimeDimIndex)=numel(TimeIndex);
+    end
+end
+
+%% get the values of the input variables
+if  ~isempty(ListVarName)
+    for ivar=1:length(var_index)
+        VarName=Data.ListVarName{ivar};
+        VarName=regexprep(VarName,'-','_'); %suppress '-' if it exists in the NetCDF variable name (leads to errors in matlab)
+        %             CheckSub=0;
+        if input_index==4% if a dimension is selected as time
+            ind_vec=zeros(1,numel(var_dim{ivar}));% vector with zeros corresponding to al the dimensions of the variable VarName
+            ind_size=dim_value(var_dim{ivar});% vector giving the size (for each dimension) of the variable VarName
+            index_time=find(var_dim{ivar}==TimeDimIndex);
+            if ~isempty(index_time)
+                if ind_size(index_time)<max(TimeIndex)
+                    errormsg=['requested index ' num2str(TimeIndex) ' exceeds matrix dimension'];
+                    return
                 end
-            end
-            ichoice=iline-1;%selected line number in the list of input names of variables
+                ind_vec(index_time)=TimeIndex-1;% selected index(or indices) to read
+                ind_size(index_time)=numel(TimeIndex);%length of the selected set of time indices
+                if numel(TimeIndex)==1 && ~strcmp(VarName,TimeVarName)
+                    Data.VarDimName{ivar}(index_time)=[];% for a single selected time remove the time in the list of dimensions (except for tTime itself)
+                end
+            end
+            Data.(VarName)=netcdf.getVar(nc,var_index(ivar)-1,ind_vec,ind_size); %read the variable data
+            Data.(VarName)=squeeze(Data.(VarName));%remove singeton dimension
         else
-            iline=1;
-        end
-        %ListVarName=ListVarName(iline,:);% select the appropriate option for input variable (lin ein the input name matrix)
-        if CheckTimeVar
-            TimeVarIndex=find(strcmp(TimeVarName,ListVarNameNetcdf),1); %look for the index of the time variable in the netcdf list
-            if isempty(TimeVarIndex)
-                errormsg='requested variable for time is missing';
-                return
-            end
-            TimeDimIndex=dimids{TimeVarIndex}(1)+1;
-            ListVarName=[ListVarName {TimeVarName}];
-        end
-        var_index=zeros(1,size(ListVarName,2));%default list of variable indices
-        for ivar=1:size(ListVarName,2)
-            search_index=find(strcmp(ListVarName{iline,ivar},ListVarNameNetcdf),1);%look for the variable name in the list of NetCDF file
-            if ~isempty(search_index)
-                var_index(ivar)=search_index;%index of the netcdf list corresponding to the input list index ivar
-            end
-        end
-        var_detect=(var_index~=0);%=1 for detected variables
-        list_index=find(var_index);% indices in the input list corresponding to a detected variable
-        var_index=var_index(list_index);% NetCDF variable indices corresponding to the output list of read variable
-        Data.ListVarName=ListVarName(1,list_index);%the first line of ListVarName sets the output names of the variables
-    end
-
-    %% get the dimensions and attributes associated to  variables
-    var_dim=cell(size(var_index));% initiate list of dimensions for variables
-    for ivar=1:length(var_index)
-        var_dim{ivar}=dimids{var_index(ivar)}+1; %netcdf dimension indices used by the variable #ivar
-        Data.VarDimName{ivar}=ListDimNameNetcdf(var_dim{ivar});
-        flag_used(var_dim{ivar})=ones(size(var_dim{ivar}));%flag_used =1 for the indices of used dimensions
-        for iatt=1:nbatt(var_index(ivar))
-            attname = netcdf.inqAttName(nc,var_index(ivar)-1,iatt-1);
-            valuestr= netcdf.getAtt(nc,var_index(ivar)-1,attname);
-            attname=regexprep(attname,{'\','/','\.','-',' '},{'','','','',''});%remove  '\','.' or '-' if exists
-            if strcmp(attname(1),'_')
-                attname(1)=[];
-            end
-            try
-                if ~isempty(valuestr)
-                    Data.VarAttribute{ivar}.(attname)=valuestr;
-                end
-            catch ME
-                display(attname)
-                display(valuestr)
-                display(ME.message)
-                Data.VarAttribute{ivar}.(['atrr_' num2str(iatt)])='not read';
-            end
-        end
-    end
-
-    %% select the dimensions used for the set of input variables
-    if ~isempty(var_index)
-        dim_index=find(flag_used);%list of netcdf dimensions indices corresponding to used dimensions
-        Data.ListDimName=ListDimNameNetcdf(dim_index);
-        Data.DimValue=dim_value(dim_index);
-        if input_index==4% if a dimension is selected as time
-            Data.DimValue(TimeDimIndex)=numel(TimeIndex);
-        end
-    end
-
-    %% get the values of the input variables
-    if  ~isempty(ListVarName)
-        for ivar=1:length(var_index)
-            VarName=Data.ListVarName{ivar};
-            VarName=regexprep(VarName,'-','_'); %suppress '-' if it exists in the NetCDF variable name (leads to errors in matlab)
-%             CheckSub=0;
-            if input_index==4% if a dimension is selected as time
-                ind_vec=zeros(1,numel(var_dim{ivar}));% vector with zeros corresponding to al the dimensions of the variable VarName
-                ind_size=dim_value(var_dim{ivar});% vector giving the size (for each dimension) of the variable VarName
-                index_time=find(var_dim{ivar}==TimeDimIndex);
-                if ~isempty(index_time)
-                    if ind_size(index_time)<max(TimeIndex)
-                        errormsg=['requested index ' num2str(TimeIndex) ' exceeds matrix dimension'];
-                        return
-                    end
-                    ind_vec(index_time)=TimeIndex-1;% selected index(or indices) to read
-                    ind_size(index_time)=numel(TimeIndex);%length of the selected set of time indices
-                    if numel(TimeIndex)==1 && ~strcmp(VarName,TimeVarName)
-                        Data.VarDimName{ivar}(index_time)=[];% for a single selected time remove the time in the list of dimensions (except for tTime itself)
-                    end
-                end
-                Data.(VarName)=netcdf.getVar(nc,var_index(ivar)-1,ind_vec,ind_size); %read the variable data
-                Data.(VarName)=squeeze(Data.(VarName));%remove singeton dimension
-            else
-                Data.(VarName)=netcdf.getVar(nc,var_index(ivar)-1); %read the whole variable data
-            end
-            if xtype(var_index(ivar))==5
-                Data.(VarName)=double(Data.(VarName)); %transform to double for single pecision
-            end
-        end
-    end
-    Data.VarType=xtype(var_index);
-
-    %%  -------- close fle-----------
-    if testfile==1
-        netcdf.close(nc)
-    end
-
-    %% old NetCDF library
-else
-    [Data,var_detect,ichoice]=nc2struct_toolbox(nc,varargin);
-end
+            Data.(VarName)=netcdf.getVar(nc,var_index(ivar)-1); %read the whole variable data
+        end
+        if xtype(var_index(ivar))==5
+            Data.(VarName)=double(Data.(VarName)); %transform to double for single pecision
+        end
+    end
+end
+Data.VarType=xtype(var_index);
+
+%%  -------- close fle-----------
+if testfile==1
+    netcdf.close(nc)
+end
+