source: trunk/src/find_field_cells.m @ 904

Last change on this file since 904 was 890, checked in by sommeria, 9 years ago

bugs solved for reading general netcdf files

File size: 16.9 KB
1%'find_field_cells': analyse the field structure for input in uvmat functions, grouping the variables  into 'fields' with common coordinates
3% function  [CellInfo,NbDim,errormsg]=find_field_cells(Data)
6% CellInfo: cell of structures describing field cells
7%     .CoordType:  type of coordinates for each field cell = 'scattered','grid','tps';
8%     .CoordIndex: array of the indices of the variables representing the coordinates (in the order z,y,x)
9%     .CoordSize: array of the nbre of values for each  coordinate in a grid, nbre of points in the unstructured case
10%     .NbCentres_tps:
11%     .SubRange_tps
12%     .VarIndex: arrays of the variable indices in the field cell
13%     .VarIndex_ancillary: indices of ancillary variables
14%              _color : color image, the last index, which is not a coordinate variable, represent the 3 color components rgb
15%              _discrete: like scalar, but set of data points without continuity, represented as dots in a usual plot, instead of continuous lines otherwise
16%              _errorflag: index of error flag
17%              _image   : B/W image, (behaves like scalar)
18%              _vector_x,_y,_z: indices of variables giving the vector components x, y, z
19%              _warnflag: index of warnflag   
20%      .ProjModeRequest= 'interp_lin', 'interp_tps' indicate whether lin interpolation  or derivatives (tps) is needed to calculate the requested field
21%      .FieldName = operation to be performed to finalise the field cell after projection
22%      .SubCheck=0 /1 indicate that the field must be substracted (second  entry in uvmat)
23% NbDim: array with the length of CellVarIndex, giving the space dimension of each field cell
24% errormsg: error message
26% INPUT:
27% Data: structure representing fields, output of check_field_structure
28%            .ListGlobalAttributes
29%            .ListVarName: cell array listing the names (cahr strings) of the variables
30%            .VarDimName: cell array of cells containing the set of dimension names for each variable of .ListVarName
31%            .VarAttribute: cell array of structures containing the variable attributes:
32%                     .VarAttribute{ilist}.key=value, where ilist is the variable
33%                     index, key is the name of the attribute, value its value (char string or number)
34%            .Attr1, .Attr2....
35%        case of actual data:
36%            .Var1, .Var2...
37%        case of data structure, without the  data themselves
38%            .LisDimName: list of dimension names
39%            .DimValue: list of corresponding dimension values
40% HELP:
41% to get the dimensions of arrays common to the field #icell
42%         VarIndex=CellVarIndex{icell}; % list of variable indices
43%         DimIndex=Data.VarDimIndex{VarIndex(1)} % list of dimensions for each variable in the cell #icell
46% Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France
48%   Joel.Sommeria - Joel.Sommeria (A)
50%     This file is part of the toolbox UVMAT.
52%     UVMAT is free software; you can redistribute it and/or modify
53%     it under the terms of the GNU General Public License as published
54%     by the Free Software Foundation; either version 2 of the license,
55%     or (at your option) any later version.
57%     UVMAT is distributed in the hope that it will be useful,
58%     but WITHOUT ANY WARRANTY; without even the implied warranty of
60%     GNU General Public License (see LICENSE.txt) for more details.
63%    group the variables  into 'fields' with common dimensions
65function [CellInfo,NbDim,errormsg]=find_field_cells(Data)
69if ~isfield(Data,'ListVarName'), errormsg='the list of variables .ListVarName is missing';return;end
70if ~isfield(Data,'VarDimName'), errormsg='the list of dimensions .VarDimName is missing';return;end
71nbvar=numel(Data.ListVarName);%number of variables in the field structure
72if ~isequal(numel(Data.VarDimName),nbvar), errormsg='.ListVarName and .VarDimName have unequal length';return;end
73% check the existence of variable data
75for ilist=1:numel(Data.ListVarName)
76    if ~isfield(Data,Data.ListVarName{ilist})
77        check_var=0;% dimensions of data defined, data not needed for this function
78        break
79    end
81if ~check_var &&  ~(isfield(Data,'ListDimName')&& isfield(Data,'DimValue')&&isequal(numel(Data.ListDimName),numel(Data.DimValue)))
82    errormsg=['missing variable or values of dimensions' Data.ListVarName{ilist}];
83    return
87%% role of variables and list of requested operations
89%   'ancillary','image','color','discrete','scalar','coord_tps'};% rmq vector_x_tps and vector_y_tps to be replaced by vector_x and vector_y
90Role=num2cell(blanks(nbvar));%initialize a cell array of nbvar blanks
91ProjModeRequest=regexprep(Role,' ',''); % fieldRequest set to '' by default
92FieldName=cell(size(Role)); % fieldRequest set to {} by default
93CheckSub=zeros(size(Role));% =1 for fields to substract
94Role=regexprep(Role,' ','scalar'); % Role set to 'scalar' by default
95if isfield(Data,'VarAttribute')
96    for ivar=1:numel(Data.VarAttribute)
97        if isfield(Data.VarAttribute{ivar},'Role')
98            Role{ivar}=Data.VarAttribute{ivar}.Role;
99        end
100        if isfield(Data.VarAttribute{ivar},'ProjModeRequest')
101            ProjModeRequest{ivar}=Data.VarAttribute{ivar}.ProjModeRequest;
102        end
103        if isfield(Data.VarAttribute{ivar},'FieldName')
104            FieldName{ivar}=Data.VarAttribute{ivar}.FieldName;
105        end
106        if isfield(Data.VarAttribute{ivar},'CheckSub')
107            CheckSub(ivar)=Data.VarAttribute{ivar}.CheckSub;
108        end
109    end
112%% find scattered (unstructured) coordinates
113ivar_coord_x=find(strcmp('coord_x',Role));%find variables with Role='coord_x'
118% loop on unstructured coordinate x -> different field cells
119for icell=1:numel(ivar_coord_x)
120    DimCell=Data.VarDimName{ivar_coord_x(icell)};% cell of dimension names for ivar_coord_x(icell)
121    if ischar(DimCell),DimCell={DimCell};end % transform char to cell for a single dimension
122    % look for variables sharing dimension(s) with ivar_coord_x(icell)
123    check_cell=zeros(numel(DimCell),nbvar);
124    for idim=1:numel(DimCell)
125        for ivar=1:nbvar
126            check_cell(idim,ivar)=max(strcmp(DimCell{idim},Data.VarDimName{ivar}));
127        end
128    end
129    check_cell=sum(check_cell,1)==numel(DimCell);%logical array=1 for variables belonging to the current cell
130    VarIndex=find(check_cell);% list of detected variable indices
131    if ~(numel(VarIndex)==1 && numel(DimCell)==1)% exclude case of isolated coord_x variable (treated later)
132        if ~(numel(VarIndex)==1 && numel(DimCell)>1)% a variable is associated to coordinate
133            CellInfo{icell}.CoordIndex=ivar_coord_x(icell);
134            % size of coordinate var
135            if check_var
136                CellInfo{icell}.CoordSize=numel(Data.(Data.ListVarName{ivar_coord_x(icell)}));
137            else
138                for idim=1:numel(DimCell)
139                    check_index= strcmp(DimCell{idim},Data.ListDimName);
140                    CellInfo{icell}.CoordSize(idim)=Data.DimValue(check_index);
141                end
142                CellInfo{icell}.CoordSize=prod(CellInfo{icell}.CoordSize);
143            end
144            ind_y=find(strcmp('coord_y',Role(VarIndex)));
145            if numel(VarIndex)==2||isempty(ind_y)% no variable, except possibly y
146                NbDim(icell)=1;
147            else
148                CellInfo{icell}.CoordType='scattered';
149                ind_z=find(strcmp('coord_z',Role(VarIndex)));
150                if numel(VarIndex)==3||isempty(ind_z)% no z variable, except possibly as a fct z(x,y)
151                    CellInfo{icell}.CoordIndex=[VarIndex(ind_y) CellInfo{icell}.CoordIndex];
152                    NbDim(icell)=2;
153                else
154                    CellInfo{icell}.CoordIndex=[VarIndex(ind_z) CellInfo{icell}.CoordIndex];
155                    NbDim(icell)=3;
156                end
157            end
158        end
159        CellInfo{icell}.VarIndex=VarIndex;
160        check_select=check_select|check_cell;
161    end
164%% look for tps coordinates
165ivar_remain=find(~check_select);% indices of remaining variables (not already selected)
166check_coord_tps= strcmp('coord_tps',Role(~check_select));
167ivar_tps=ivar_remain(check_coord_tps);% variable indices corresponding to tps coordinates
169% loop on the tps coordinate sets
170for icell_tps=1:numel(ivar_tps)
171    check_cell=zeros(1,nbvar);% =1 for the variables selected in the current cell
172    check_cell(ivar_tps(icell_tps))=1;% mark the coordinate variable as selected
173    DimCell=Data.VarDimName{ivar_tps(icell_tps)};% dimension names for the current tps coordinate variable
174    icell=numel(CellInfo)+icell_tps; % new field cell index
175    CellInfo{icell}.CoordIndex=ivar_tps(icell_tps);% index of the  tps coordinate variable
176    if numel(DimCell)==3
177        VarDimName=Data.VarDimName(~check_select);
178        for ivardim=1:numel(VarDimName)
179            if strcmp(VarDimName{ivardim},DimCell{3})
180                CellInfo{icell}.NbCentres_tps= ivar_remain(ivardim);% nbre of sites for each tps subdomain
181                check_cell(ivar_remain(ivardim))=1;% mark the variable as selected
182            elseif strcmp(VarDimName{ivardim}{1},DimCell{2}) && numel(VarDimName{ivardim})>=3 && strcmp(VarDimName{ivardim}{3},DimCell{3})
183                CellInfo{icell}.SubRange_tps=ivar_remain(ivardim);% subrange definiton for tps
184                check_cell(ivar_remain(ivardim))=1;% mark the variable as selected
185            elseif strcmp(VarDimName{ivardim}{1},DimCell{1}) && strcmp(VarDimName{ivardim}{2},DimCell{3})% variable
186                check_cell(ivar_remain(ivardim))=1;% mark the variable as selected
187            end
188        end
189    end
190    CellInfo{icell}.CoordType='tps';
191    CellInfo{icell}.VarIndex=find(check_cell);
192    if check_var
193        NbDim(icell)=size(Data.(Data.ListVarName{CellInfo{icell}.CoordIndex}),2);
194        CellInfo{icell}.CoordSize=size(Data.(Data.ListVarName{CellInfo{icell}.CoordIndex}),1)*size(Data.(Data.ListVarName{CellInfo{icell}.CoordIndex}),3);
195    else
196        check_index_1= strcmp(DimCell{1},Data.ListDimName);
197        check_index_2= strcmp(DimCell{2},Data.ListDimName);
198        NbDim(icell)=Data.DimValue(check_index_2);
199        if numel(DimCell)>=3
200        check_index_3= strcmp(DimCell{3},Data.ListDimName); 
201        CellInfo{icell}.CoordSize=Data.DimValue(check_index_1)*Data.DimValue(check_index_3);
202        end
203    end
204    check_select=check_select|check_cell;
207%% look for coordinate variables and corresponding gridded data:
208% coordinate variables are variables associated with a single dimension, defining the coordinate values
209% two cases: 1)the coordiante variable represents the set of coordiante values
210%            2)the coordinate variable contains only two elements, representing the coordinate bounds for the dimension with the same name as the cordinate
211ivar_remain=find(~check_select);% indices of remaining variables, not already taken into account
212ListVarName=Data.ListVarName(~check_select);%list of names of remaining variables
213VarDimName=Data.VarDimName(~check_select);%dimensions of remaining variables
214check_coord_select= cellfun(@numel,VarDimName)==1|cellfun(@ischar,VarDimName)==1;% find remaining variables with a single dimension
215check_coord_select=check_coord_select & ~strcmp('ancillary',Role(~check_select));% do not select ancillary variables as coordinates
216ListCoordIndex=ivar_remain(check_coord_select);% indices of remaining variables with a single dimension
217ListCoordName=ListVarName(check_coord_select);% corresponding names of remaining variables with a single dimension
218ListDimName=VarDimName(check_coord_select);% dimension names of remaining variables with a single dimension
220%remove redondant variables -> keep only one variable per dimension
222for idim=1:numel(ListDimName)
223    prev_ind=find(strcmp(ListDimName{idim},ListDimName(1:idim-1)));% check whether the dimension is already taken into account
224    if ~isempty(prev_ind)% in case of multiple coord variable
225        if strcmp(ListCoordName{idim},ListDimName{idim}) %variable with the same name as the coordinate taken in priority
226            check_keep(prev_ind)=0;% choose a variable with the same name as coordinate in priority
227        else
228           check_keep(idim)=0; %keep the first coordiante variable found
229        end
230    end
232ListCoordIndex=ListCoordIndex(check_keep);% list of coordinate variable indices
233ListCoordName=ListCoordName(check_keep);% list of coordinate variable names
234ListDimName=ListDimName(check_keep);% list of coordinate dimension names
236% determine dimension sizes
238for ilist=1:numel(ListCoordIndex)
239    if iscell(ListDimName{ilist})
240        ListDimName(ilist)=ListDimName{ilist};%transform cell to string
241    end
242    if check_var% if the list of dimensions has been directly defined, no variable data available
243        CoordSize(ilist)=numel(Data.(ListCoordName{ilist}));% number of elements in the variable corresponding to the dimension #ilist
244    else
245        check_index= strcmp(ListDimName{ilist},Data.ListDimName);% find the  index in the list of dimensions
246        CoordSize(ilist)=Data.DimValue(check_index);% find the  corresponding dimension value
247    end
248    if CoordSize(ilist)==2% case of uniform grid coordinate defined by lower and upper bounds only
249        ListDimName{ilist}=ListCoordName{ilist};% replace the dimension name by the coordinate variable name
250    end
253%% group the remaining variables in cells sharing the same coordinate variables
257for ivardim=1:numel(VarDimName) % loop at the list of dimensions for the remaining variables
258    DimCell=VarDimName{ivardim};% dimension names of the current variable
259    if ischar(DimCell), DimCell={DimCell}; end %transform char to cell if needed
260    DimIndices=[];
261    for idim=1:numel(DimCell)
262        ind_dim=find(strcmp(DimCell{idim},ListDimName));%find the dim index in the list of dimensions ListDimName
263        if ~isempty(ind_dim)
264            DimIndices=[DimIndices ind_dim]; %update the list of dim indices included in DimCell
265            if check_var && CoordSize(ind_dim)==2 % determine the size of the coordinate in case of coordinate definition limited to lower and upper bounds
266                if isvector(Data.(ListVarName{ivardim}))
267                    if numel(Data.(ListVarName{ivardim}))>2
268                        CoordSize(ind_dim)=numel(Data.(ListVarName{ivardim}));
269                    end
270                else
271                    CoordSize(ind_dim)=size(Data.(ListVarName{ivardim}),idim);
272                end
273            end
274        end
275    end
276    % look for cells of variables with the same coordinate variables
277    check_previous=0;
278    for iprev=1:numel(NewCellInfo)
279        if isequal(DimIndices,NewCellDimIndex{iprev})
280            check_previous=1;
281            NewCellInfo{iprev}.VarIndex=[NewCellInfo{iprev}.VarIndex ivar_remain(ivardim)];%append the current variable index to the found field cell
282            break
283        end
284    end
285    % create a new cell if no previous one contains the coordinate variables
286    if ~check_previous
287        nbcell=numel(NewCellInfo)+1;
288        NewCellDimIndex{nbcell}=DimIndices;
289        NewCellInfo{nbcell}.VarIndex=ivar_remain(ivardim);% create a new field cell with the current variable index
290        NewNbDim(nbcell)=numel(DimIndices);
291        NewCellInfo{nbcell}.CoordType='grid';
292        NewCellInfo{nbcell}.CoordSize=CoordSize(DimIndices);
293        NewCellInfo{nbcell}.CoordIndex=ListCoordIndex(DimIndices);
294    end
296NbDim=[NbDim NewNbDim];
297CellInfo=[CellInfo NewCellInfo];
299%% suppress empty cells or cells with a single coordinate variable
301for icell=1:numel(check_remove)
302    if isempty(CellInfo{icell})||(numel(CellInfo{icell}.VarIndex)==1 && check_coord(icell))
303        check_remove(icell)=1;
304    end
309%% document roles of non-coordinate variables
310for icell=1:numel(CellInfo)
311    VarIndex=CellInfo{icell}.VarIndex;
312    for ivar=VarIndex
313        if isfield(CellInfo{icell},['VarIndex_' Role{ivar}])
314            CellInfo{icell}.(['VarIndex_' Role{ivar}])=[CellInfo{icell}.(['VarIndex_' Role{ivar}]) ivar];
315        else
316            CellInfo{icell}.(['VarIndex_' Role{ivar}])= ivar;
317        end
318        if ~isempty(ProjModeRequest{ivar})
319            CellInfo{icell}.ProjModeRequest=ProjModeRequest{ivar};
320        end
321        if ~isempty(FieldName{ivar})
322            CellInfo{icell}.FieldName=FieldName{ivar};
323        end
324        if CheckSub(ivar)==1
325            CellInfo{icell}.CheckSub=1;
326        end
327    end
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