source: trunk/src/nc2struct.m @ 809

%'nc2struct': transform a netcdf file in a corresponding matlab structure
% it reads all the global attributes and all variables, or a selected list.
% The corresponding dimensions and variable attributes are then extracted
%----------------------------------------------------------------------
% function [Data,var_detect,ichoice,errormsg]=nc2struct(nc,varargin)
%
% OUTPUT:
%  Data: structure containing all the information of the netcdf file (or netcdf object)
%           with (optional)fields:
%                    .ListGlobalAttribute: cell listing the names of the global attributes
%                    .Att_1,Att_2... : values of the global attributes
%                    .ListVarName: list of variable names to select (cell array of  char strings {'VarName1', 'VarName2',...} ) 
%                    .VarDimName: list of dimension names for each element of .ListVarName (cell array of string cells)                         
%                    .Var1, .Var2....: variables (Matlab arrays) with names listed in .ListVarName
%                  .ListDimName=list of dimension (added information, not requested for field description)
%                  .DimValue= vlalues of dimensions (added information, not requested for field description)
%                  .VarType= integers giving the type of variable as coded by netcdf= 2 for char, =4 for single,=( for double
%  var_detect: vector with same length as the cell array ListVarName, = 1 for each detected variable and 0 else.
%            var_detect=[] in the absence of input cell array 
%  ichoice: index of the selected line in the case of multiple choice 
%        (cell array of varible names with multiple lines) , =[] by default 
%INPUT:
%  nc:  name of a netcdf file (char string) or netcdf object   
%  additional arguments:
%       -no additional arguments: all the variables of the netcdf file are read.
%       -a cell array, ListVarName, made of  char strings {'VarName1', 'VarName2',...} ) 
%         if ListVarName=[] or {}, no variable value is read (only global attributes and list of variables and dimensions)
%         if ListVarName is absent, or = '*', ALL the variables of the netcdf file are read. 
%         if ListVarName is a cell array with n lines, the set of variables will be sought by order of priority in the list,
%            while output names will be set by the first line
%       - the string 'ListGlobalAttribute' followed by a list of attribute  names: reads only these attributes (fast reading)
%       - the string 'TimeVarName', a string (the name of the variable considered as time), an integer or vector with integer values 
%            representing time indices to select for each variable, the cell of other input variable names.
%       - the string 'TimeDimName', a string (the name of the dimension considered as time), an integer or vector with integer values 
%            representing time indices to select for each variable, the cell of other input variable names.

%=======================================================================
% Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France
%   http://www.legi.grenoble-inp.fr
%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
%
%     This file is part of the toolbox UVMAT.
%
%     UVMAT is free software; you can redistribute it and/or modify
%     it under the terms of the GNU General Public License as published
%     by the Free Software Foundation; either version 2 of the license,
%     or (at your option) any later version.
%
%     UVMAT is distributed in the hope that it will be useful,
%     but WITHOUT ANY WARRANTY; without even the implied warranty of
%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
%     GNU General Public License (see LICENSE.txt) for more details.
%=======================================================================
   
function [Data,var_detect,ichoice,errormsg]=nc2struct(nc,varargin)
errormsg='';%default error message
if isempty(varargin)
    varargin{1}='*';
end
hhh=which('netcdf.open');% look for built-in matlab netcdf library

if ~isequal(hhh,'')
    %% default output
    Data=[];%default
    var_detect=[];%default
    ichoice=[];%default
    
    %% open the netcdf file for reading
    if ischar(nc)
        if exist(nc,'file')
            try
                nc=netcdf.open(nc,'NC_NOWRITE');
                testfile=1;
            catch ME
                errormsg=['ERROR opening ' nc ': ' ME.message];
                return
            end
        else
            errormsg=['ERROR:file ' nc ' does not exist'];
            return
        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 varibles 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
            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)=double(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