source: trunk/src/find_field_cells.m @ 1024

Last change on this file since 1024 was 1024, checked in by sommeria, 6 years ago

pb for reading images repaired

File size: 16.8 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 2008-2017, LEGI UMR 5519 / CNRS UGA 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 array defined, but the corresponding array is not given
78        break
79    end
82%% role of variables and list of requested operations
84%   'ancillary','image','color','discrete','scalar','coord_tps'};% rmq vector_x_tps and vector_y_tps to be replaced by vector_x and vector_y
85Role=num2cell(blanks(nbvar));%initialize a cell array of nbvar blanks
86ProjModeRequest=regexprep(Role,' ',''); % fieldRequest set to '' by default
87FieldName=cell(size(Role)); % fieldRequest set to {} by default
88CheckSub=zeros(size(Role));% =1 for fields to substract
89Role=regexprep(Role,' ','scalar'); % Role set to 'scalar' by default
90if isfield(Data,'VarAttribute')
91    for ivar=1:numel(Data.VarAttribute)
92        if isfield(Data.VarAttribute{ivar},'Role')
93            Role{ivar}=Data.VarAttribute{ivar}.Role;
94        end
95        if isfield(Data.VarAttribute{ivar},'ProjModeRequest')
96            ProjModeRequest{ivar}=Data.VarAttribute{ivar}.ProjModeRequest;
97        end
98        if isfield(Data.VarAttribute{ivar},'FieldName')
99            FieldName{ivar}=Data.VarAttribute{ivar}.FieldName;
100        end
101        if isfield(Data.VarAttribute{ivar},'CheckSub')
102            CheckSub(ivar)=Data.VarAttribute{ivar}.CheckSub;
103        end
104    end
107%% find scattered (unstructured) coordinates
108ivar_coord_x=find(strcmp('coord_x',Role));%find variables with Role='coord_x'
113% loop on unstructured coordinate x -> different field cells
114for icell=1:numel(ivar_coord_x)
115    DimCell=Data.VarDimName{ivar_coord_x(icell)};% cell of dimension names for ivar_coord_x(icell)
116    if ischar(DimCell),DimCell={DimCell};end % transform char to cell for a single dimension
117    % look for variables sharing dimension(s) with ivar_coord_x(icell)
118    check_cell=zeros(numel(DimCell),nbvar);
119    for idim=1:numel(DimCell);% for each variable with role coord_x, look at which other variables contain the same dimension
120        for ivar=1:nbvar
121            check_cell(idim,ivar)=max(strcmp(DimCell{idim},Data.VarDimName{ivar}));
122        end
123    end
124    check_cell=sum(check_cell,1)==numel(DimCell);%logical array=1 for variables belonging to the current cell
125    VarIndex=find(check_cell);% list of detected variable indices
126    if ~(numel(VarIndex)==1 && numel(DimCell)==1)% exclude case of isolated coord_x variable (treated later)
127        if ~(numel(VarIndex)==1 && numel(DimCell)>1)% a variable is associated to coordinate
128            CellInfo{icell}.CoordIndex=ivar_coord_x(icell);
129            % size of coordinate var
130            if check_var
131                CellInfo{icell}.CoordSize=numel(Data.(Data.ListVarName{ivar_coord_x(icell)}));
132            else
133                for idim=1:numel(DimCell)
134                    check_index= strcmp(DimCell{idim},Data.ListDimName);
135                    CellInfo{icell}.CoordSize(idim)=Data.DimValue(check_index);
136                end
137                CellInfo{icell}.CoordSize=prod(CellInfo{icell}.CoordSize);
138            end
139            ind_y=find(strcmp('coord_y',Role(VarIndex)));
140            if numel(VarIndex)==2||isempty(ind_y)% no variable, except possibly y
141                NbDim(icell)=1;
142            else
143                CellInfo{icell}.CoordType='scattered';
144                ind_z=find(strcmp('coord_z',Role(VarIndex)));
145                if numel(VarIndex)==3||isempty(ind_z)% no z variable, except possibly as a fct z(x,y)
146                    CellInfo{icell}.CoordIndex=[VarIndex(ind_y) CellInfo{icell}.CoordIndex];
147                    NbDim(icell)=2;
148                else
149                    CellInfo{icell}.CoordIndex=[VarIndex(ind_z) CellInfo{icell}.CoordIndex];
150                    NbDim(icell)=3;
151                end
152            end
153        end
154        CellInfo{icell}.VarIndex=VarIndex;
155        check_select=check_select|check_cell;
156    end
159%% look for tps coordinates
160ivar_remain=find(~check_select);% indices of remaining variables (not already selected)
161check_coord_tps= strcmp('coord_tps',Role(~check_select));
162ivar_tps=ivar_remain(check_coord_tps);% variable indices corresponding to tps coordinates
164% loop on the tps coordinate sets
165for icell_tps=1:numel(ivar_tps)
166    check_cell=zeros(1,nbvar);% =1 for the variables selected in the current cell
167    check_cell(ivar_tps(icell_tps))=1;% mark the coordinate variable as selected
168    DimCell=Data.VarDimName{ivar_tps(icell_tps)};% dimension names for the current tps coordinate variable
169    icell=numel(CellInfo)+icell_tps; % new field cell index
170    CellInfo{icell}.CoordIndex=ivar_tps(icell_tps);% index of the  tps coordinate variable
171    if numel(DimCell)==3
172        VarDimName=Data.VarDimName(~check_select);
173        for ivardim=1:numel(VarDimName)
174            if strcmp(VarDimName{ivardim},DimCell{3})
175                CellInfo{icell}.NbCentres_tps= ivar_remain(ivardim);% nbre of sites for each tps subdomain
176                check_cell(ivar_remain(ivardim))=1;% mark the variable as selected
177            elseif strcmp(VarDimName{ivardim}{1},DimCell{2}) && numel(VarDimName{ivardim})>=3 && strcmp(VarDimName{ivardim}{3},DimCell{3})
178                CellInfo{icell}.SubRange_tps=ivar_remain(ivardim);% subrange definiton for tps
179                check_cell(ivar_remain(ivardim))=1;% mark the variable as selected
180            elseif strcmp(VarDimName{ivardim}{1},DimCell{1}) && strcmp(VarDimName{ivardim}{2},DimCell{3})% variable
181                check_cell(ivar_remain(ivardim))=1;% mark the variable as selected
182            end
183        end
184    end
185    CellInfo{icell}.CoordType='tps';
186    CellInfo{icell}.VarIndex=find(check_cell);
187    if check_var
188        NbDim(icell)=size(Data.(Data.ListVarName{CellInfo{icell}.CoordIndex}),2);
189        CellInfo{icell}.CoordSize=size(Data.(Data.ListVarName{CellInfo{icell}.CoordIndex}),1)*size(Data.(Data.ListVarName{CellInfo{icell}.CoordIndex}),3);
190    else
191        check_index_1= strcmp(DimCell{1},Data.ListDimName);
192        check_index_2= strcmp(DimCell{2},Data.ListDimName);
193        NbDim(icell)=Data.DimValue(check_index_2);
194        if numel(DimCell)>=3
195        check_index_3= strcmp(DimCell{3},Data.ListDimName); 
196        CellInfo{icell}.CoordSize=Data.DimValue(check_index_1)*Data.DimValue(check_index_3);
197        end
198    end
199    check_select=check_select|check_cell;
202%% look for coordinate variables and corresponding gridded data:
203% coordinate variables are variables associated with a single dimension, defining the coordinate values
204% two cases: 1)the coordiante variable represents the set of coordiante values
205%            2)the coordinate variable contains only two elements, representing the coordinate bounds for the dimension with the same name as the cordinate
206ivar_remain=find(~check_select);% indices of remaining variables, not already taken into account
207ListVarName=Data.ListVarName(~check_select);%list of names of remaining variables
208VarDimName=Data.VarDimName(~check_select);%dimensions of remaining variables
209check_coord_select= cellfun(@numel,VarDimName)==1|cellfun(@ischar,VarDimName)==1;% find remaining variables with a single dimension
210check_coord_select=check_coord_select & ~strcmp('ancillary',Role(~check_select));% do not select ancillary variables as coordinates
211ListCoordIndex=ivar_remain(check_coord_select);% indices of remaining variables with a single dimension
212ListCoordName=ListVarName(check_coord_select);% corresponding names of remaining variables with a single dimension
213ListDimName=VarDimName(check_coord_select);% dimension names of remaining variables with a single dimension
215%remove redondant variables -> keep only one variable per dimension
217for idim=1:numel(ListDimName)
218    prev_ind=find(strcmp(ListDimName{idim},ListDimName(1:idim-1)));% check whether the dimension is already taken into account
219    if ~isempty(prev_ind)% in case of multiple coord variable
220        if strcmp(ListCoordName{idim},ListDimName{idim}) %variable with the same name as the coordinate taken in priority
221            check_keep(prev_ind)=0;% choose a variable with the same name as coordinate in priority
222        else
223           check_keep(idim)=0; %keep the first coordiante variable found
224        end
225    end
227ListCoordIndex=ListCoordIndex(check_keep);% list of coordinate variable indices
228ListCoordName=ListCoordName(check_keep);% list of coordinate variable names
229ListDimName=ListDimName(check_keep);% list of coordinate dimension names
231% determine dimension sizes
233for ilist=1:numel(ListCoordIndex)
234    if iscell(ListDimName{ilist})
235        ListDimName(ilist)=ListDimName{ilist};%transform cell to string
236    end
237    if check_var% if the list of dimensions has been directly defined, no variable data available
238        CoordSize(ilist)=numel(Data.(ListCoordName{ilist}));% number of elements in the variable corresponding to the dimension #ilist
239    else
240        check_index= strcmp(ListDimName{ilist},Data.ListDimName);% find the  index in the list of dimensions
241        CoordSize(ilist)=Data.DimValue(check_index);% find the  corresponding dimension value
242    end
243    if CoordSize(ilist)==2% case of uniform grid coordinate defined by lower and upper bounds only
244        ListDimName{ilist}=ListCoordName{ilist};% replace the dimension name by the coordinate variable name
245    end
248%% group the remaining variables in cells sharing the same coordinate variables
252for ivardim=1:numel(VarDimName) % loop at the list of dimensions for the remaining variables
253    DimCell=VarDimName{ivardim};% dimension names of the current variable
254    if ischar(DimCell), DimCell={DimCell}; end %transform char to cell if needed
255    DimIndices=[];
256    for idim=1:numel(DimCell)
257        ind_dim=find(strcmp(DimCell{idim},ListDimName));%find the dim index in the list of dimensions ListDimName
258        if ~isempty(ind_dim)
259            DimIndices=[DimIndices ind_dim]; %update the list of dim indices included in DimCell
260            if check_var & CoordSize(ind_dim)==2 % determine the size of the coordinate in case of coordinate definition limited to lower and upper bounds
261                if isvector(Data.(ListVarName{ivardim}))
262                    if numel(Data.(ListVarName{ivardim}))>2
263                        CoordSize(ind_dim)=numel(Data.(ListVarName{ivardim}));
264                    end
265                else
266                    CoordSize(ind_dim)=size(Data.(ListVarName{ivardim}),idim);
267                end
268            end
269        end
270    end
271    % look for cells of variables with the same coordinate variables
272    check_previous=0;
273    for iprev=1:numel(NewCellInfo)
274        if isequal(DimIndices,NewCellDimIndex{iprev})
275            check_previous=1;
276            NewCellInfo{iprev}.VarIndex=[NewCellInfo{iprev}.VarIndex ivar_remain(ivardim)];%append the current variable index to the found field cell
277            break
278        end
279    end
280    % create a new cell if no previous one contains the coordinate variables
281    if ~check_previous
282        nbcell=numel(NewCellInfo)+1;
283        NewCellDimIndex{nbcell}=DimIndices;
284        NewCellInfo{nbcell}.VarIndex=ivar_remain(ivardim);% create a new field cell with the current variable index
285        NewNbDim(nbcell)=numel(DimIndices);
286        NewCellInfo{nbcell}.CoordType='grid';
287        NewCellInfo{nbcell}.CoordSize=CoordSize(DimIndices);
288        NewCellInfo{nbcell}.CoordIndex=ListCoordIndex(DimIndices);
289    end
291NbDim=[NbDim NewNbDim];
292CellInfo=[CellInfo NewCellInfo];
294%% suppress empty cells or cells with a single coordinate variable
296for icell=1:numel(check_remove)
297    if isempty(CellInfo{icell})||(numel(CellInfo{icell}.VarIndex)==1 && numel(check_coord)>=icell && check_coord(icell))
298        check_remove(icell)=1;
299    end
304%% document roles of non-coordinate variables
305for icell=1:numel(CellInfo)
306    VarIndex=CellInfo{icell}.VarIndex;
307    for ivar=VarIndex
308        if isfield(CellInfo{icell},['VarIndex_' Role{ivar}])
309            CellInfo{icell}.(['VarIndex_' Role{ivar}])=[CellInfo{icell}.(['VarIndex_' Role{ivar}]) ivar];
310        else
311            CellInfo{icell}.(['VarIndex_' Role{ivar}])= ivar;
312        end
313        if ~isempty(ProjModeRequest{ivar})
314            CellInfo{icell}.ProjModeRequest=ProjModeRequest{ivar};
315        end
316        if ~isempty(FieldName{ivar})
317            CellInfo{icell}.FieldName=FieldName{ivar};
318        end
319        if CheckSub(ivar)==1
320            CellInfo{icell}.CheckSub=1;
321        end
322    end
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