source: trunk/src/read_field.m @ 952

Last change on this file since 952 was 924, checked in by g7moreau, 5 years ago
  • Update Copyright Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
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1%'read_field': read the fields from files in different formats (netcdf files, images, video)
2%--------------------------------------------------------------------------
3%  function [Field,ParamOut,errormsg] = read_field(FileName,FileType,ParamIn,num)
4%
5% OUTPUT:
6% Field: matlab structure representing the field
7% ParamOut: structure representing parameters:
8%        .FieldName; field name
9%        .VelType
10%        .CivStage: stage of civx processing (=0, not Civx, =1 (civ1), =2  (fix1)....     
11%        .Npx,.Npy: for images, nbre of pixels in x and y
12% errormsg: error message, ='' by default
13%
14%INPUT
15% FileName: name of the input file
16% FileType: type of file, as determined by the function get_file_info.m
17% ParamIn: movie object or Matlab structure of input parameters
18%     .FieldName: name (char string) of the input field (for Civx data)
19%     .VelType: char string giving the type of velocity data ('civ1', 'filter1', 'civ2'...)
20%     .ColorVar: variable used for vector color
21%     .Npx, .Npy: nbre of pixels along x and y (used for .vol input files)
22%     .TimeDimName: name of the dimension considered as 'time', selected index value then set by input 'num'   
23% num: frame number for movies
24%
25% see also read_image.m,read_civxdata.m,read_civdata.m,
26
27%=======================================================================
28% Copyright 2008-2016, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
29%   http://www.legi.grenoble-inp.fr
30%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
31%
32%     This file is part of the toolbox UVMAT.
33%
34%     UVMAT is free software; you can redistribute it and/or modify
35%     it under the terms of the GNU General Public License as published
36%     by the Free Software Foundation; either version 2 of the license,
37%     or (at your option) any later version.
38%
39%     UVMAT is distributed in the hope that it will be useful,
40%     but WITHOUT ANY WARRANTY; without even the implied warranty of
41%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
42%     GNU General Public License (see LICENSE.txt) for more details.
43%=======================================================================
44
45function [Field,ParamOut,errormsg] = read_field(FileName,FileType,ParamIn,num)
46%% default output and check input
47Field=[];
48if ~exist('num','var')
49    num=1;
50end
51if ~exist('ParamIn','var')
52    ParamIn=[];
53end
54ParamOut=ParamIn;%default
55errormsg='';
56if ~exist(FileName,'file')
57    errormsg=['input file ' FileName ' does not exist'];
58    return
59end
60A=[];
61InputField={};
62check_colorvar=0;
63if isstruct(ParamIn)
64    if isfield(ParamIn,'FieldName')
65        if ischar(ParamIn.FieldName)
66            InputField={ParamIn.FieldName};
67        else
68            InputField= ParamIn.FieldName;
69        end
70    end
71    check_colorvar=zeros(size(InputField));
72    if isfield(ParamIn,'ColorVar')&&~isempty(ParamIn.ColorVar)
73        InputField=[ParamIn.FieldName {ParamIn.ColorVar}];
74        check_colorvar(numel(InputField))=1;
75    end
76end
77
78%% distingush different input file types
79switch FileType
80    case 'civdata'% new format for civ results
81        [Field,ParamOut.VelType,errormsg]=read_civdata(FileName,InputField,ParamIn.VelType);
82        if ~isempty(errormsg),errormsg=['read_civdata / ' errormsg];return,end
83        ParamOut.CivStage=Field.CivStage;
84    case 'civx'% old (obsolete) format for civ results
85        ParamOut.FieldName='velocity';%Civx data found, set .FieldName='velocity' by default
86        [Field,ParamOut.VelType,errormsg]=read_civxdata(FileName,InputField,ParamIn.VelType);
87        if ~isempty(errormsg),errormsg=['read_civxdata / ' errormsg];return,end
88        ParamOut.CivStage=Field.CivStage;
89    case 'netcdf'% general netcdf file (not recognized as civ)
90        ListVar={};
91        Role={};
92        ProjModeRequest={};
93        ListInputField={};
94        ListOperator={};
95        checkU=0;
96        checkV=0;
97        for ilist=1:numel(InputField)
98            % look for input variables to read
99            r=regexp(InputField{ilist},'(?<Operator>(^vec|^norm))\((?<UName>.+),(?<VName>.+)\)$','names');
100            if isempty(r)%  no operator used
101                if isempty(find(strcmp(InputField{ilist},ListVar)))
102                    ListVar=[ListVar InputField(ilist)];%append the variable name if not already in the list
103                    ListInputField=[ListInputField InputField(ilist)];
104                    ListOperator=[ListOperator {''}];
105                end
106                if check_colorvar(ilist)
107                    if isempty(find(strcmp(InputField{ilist},ListVar)))
108                    Role{numel(ListVar)}='ancillary';% not projected with interpolation
109                    ProjModeRequest{numel(ListVar)}='';
110                    end
111                else
112                    Role{numel(ListVar)}='scalar';
113                    ProjModeRequest{numel(ListVar)}='interp_lin';%scalar field (requires interpolation for plot)
114                end
115            else  % an operator 'vec' or 'norm' is used
116                if ~check_colorvar(ilist) && strcmp(r.Operator,'norm')
117                    ProjModeRequestVar='interp_lin';%scalar field (requires interpolation for plot)
118                else
119                    ProjModeRequestVar='';
120                end
121                ind_var_U=find(strcmp(r.UName,ListVar));%check previous listing of variable r.UName
122                ind_var_V=find(strcmp(r.VName,ListVar));%check previous listing of variable r.VName
123                if isempty(ind_var_U)
124                    ListVar=[ListVar {r.UName}]; % append the variable in the list if not previously listed
125                    Role=[Role {'vector_x'}];
126                    ProjModeRequest=[ProjModeRequest {ProjModeRequestVar}];
127                    ListInputField=[ListInputField InputField(ilist)];
128                else
129                    checkU=1;
130                end
131                if isempty(ind_var_V)
132                    ListVar=[ListVar {r.VName}];% append the variable in the list if not previously listed
133                    Role=[Role {'vector_y'}];
134                    ProjModeRequest=[ProjModeRequest {ProjModeRequestVar}];
135                    ListInputField=[ListInputField InputField(ilist)];
136                   
137                else
138                    checkV=1;
139                end
140            end
141        end
142        if ~isfield(ParamIn,'Coord_z')
143            ParamIn.Coord_z=[];
144        end
145        NbCoord=~isempty(ParamIn.Coord_x)+~isempty(ParamIn.Coord_y)+~isempty(ParamIn.Coord_z);
146        if isfield(ParamIn,'TimeDimName')% case of reading of a single time index in a multidimensional array
147            [Field,var_detect,ichoice,errormsg]=nc2struct(FileName,'TimeDimName',ParamIn.TimeDimName,num,[ParamIn.Coord_x ParamIn.Coord_y ParamIn.Coord_z ListVar]);
148        elseif isfield(ParamIn,'TimeVarName')% case of reading of a single time  in a multidimensional array
149            [Field,var_detect,ichoice,errormsg]=nc2struct(FileName,'TimeVarName',ParamIn.TimeVarName,num,[ParamIn.Coord_x ParamIn.Coord_y ParamIn.Coord_z ListVar]);
150            if numel(num)~=1
151                NbCoord=NbCoord+1;% adds time coordinate, except if q single time hqs been selected
152            end
153        else
154            [Field,var_detect,ichoice,errormsg]=nc2struct(FileName,[ParamIn.Coord_x ParamIn.Coord_y ParamIn.Coord_z ListVar]);
155        end
156        if ~isempty(errormsg)
157            return
158        end
159        %scan all the variables beyond the two first ones, ParamIn.Coord_x and ParamIn.Coord_y.
160        for ilist=NbCoord+1:numel(Field.VarDimName)
161            if isequal(Field.VarDimName{1},Field.VarDimName{ilist}) % if a variable has the same dimension as the coordinate, it denotes a field with unstructured coordinates
162                Field.VarAttribute{1}.Role='coord_x';%unstructured coordinates
163                Field.VarAttribute{2}.Role='coord_y';
164                if NbCoord>=3
165                    Field.VarAttribute{3}.Role='coord_z';
166                end
167                break
168            end
169        end
170        NormName='';
171        UName='';
172        VName='';
173        if numel(Field.ListVarName)>NbCoord % if there are variables beyond coord (1 D plots)
174            for ilist=1:numel(ListVar)
175                Field.VarAttribute{ilist+NbCoord}.Role=Role{ilist};
176                Field.VarAttribute{ilist+NbCoord}.ProjModeRequest=ProjModeRequest{ilist};
177                if isfield(ParamIn,'FieldName')
178                    Field.VarAttribute{ilist+NbCoord}.FieldName=ListInputField{ilist};
179                end
180                r=regexp(ListInputField{ilist},'(?<Operator>(^vec|^norm))\((?<UName>.+),(?<VName>.+)\)$','names');
181                if ~isempty(r)&& strcmp(r.Operator,'norm')
182                    NormName='norm';
183                    if ~isempty(find(strcmp(ListVar,'norm')))
184                        NormName='norm_1';
185                    end
186                    Field.ListVarName=[Field.ListVarName {NormName}];
187                    ilistmax=numel(Field.ListVarName);
188                    Field.VarDimName{ilistmax}=Field.VarDimName{ilist+2};
189                    Field.VarAttribute{ilistmax}.Role='scalar';
190                    Field.(NormName)=Field.(r.UName).*Field.(r.UName)+Field.(r.VName).*Field.(r.VName);
191                    Field.(NormName)=sqrt(Field.(NormName));
192                    UName=r.UName;
193                    VName=r.VName;
194                end
195            end
196           
197            if ~isempty(NormName)% remove U and V if norm has been calculated and U and V are not needed as variables
198                ind_var_U=find(strcmp(UName,ListVar));%check previous listing of variable r.UName
199                ind_var_V=find(strcmp(VName,ListVar));%check previous listing of variable r.VName
200                if ~checkU && ~checkV
201                    Field.ListVarName([ind_var_U+2 ind_var_V+2])=[];
202                    Field.VarDimName([ind_var_U+2 ind_var_V+2])=[];
203                    Field.VarAttribute([ind_var_U+2 ind_var_V+2])=[];
204                elseif ~checkU
205                    Field.ListVarName(ind_var_U+2)=[];
206                    Field.VarDimName(ind_var_U+2)=[];
207                    Field.VarAttribute(ind_var_U+2 )=[];
208                elseif ~checkV
209                    Field.ListVarName(ind_var_V+2)=[];
210                    Field.VarDimName(ind_var_V+2)=[];
211                    Field.VarAttribute(ind_var_V+2 )=[];
212                end
213            end
214            % insert coordinates as indices in case of plots vs matrix index
215            if isfield(ParamIn,'CheckCoordIndex') && ParamIn.CheckCoordIndex
216                Field.ListVarName=[Field.ListDimName Field.ListVarName];
217                Field.VarDimName=[Field.ListDimName Field.VarDimName];
218                for idim=1:numel(Field.ListDimName)
219                    CoordName=Field.ListDimName{idim};
220                    Field.(CoordName)=1:Field.DimValue(idim);
221                end
222                Field.VarAttribute=[cell(1,numel(Field.ListDimName)) Field.VarAttribute];
223            end
224        end
225    case 'video'
226        if strcmp(class(ParamIn),'VideoReader')
227            A=read(ParamIn,num);
228        else
229            ParamOut=VideoReader(FileName);
230            A=read(ParamOut,num);
231        end
232    case 'mmreader'
233        if strcmp(class(ParamIn),'mmreader')
234            A=read(ParamIn,num);
235        else
236            ParamOut=mmreader(FileName);
237            A=read(ParamOut,num);
238        end
239    case 'vol'
240        A=imread(FileName);
241        Npz=size(A,1)/ParamIn.Npy;
242        A=reshape(A',ParamIn.Npx,ParamIn.Npy,Npz);
243        A=permute(A,[3 2 1]);
244    case 'multimage'
245        %  warning 'off'
246        A=imread(FileName,num);
247    case 'image'
248        A=imread(FileName);
249    case 'rdvision'
250        [A,FileInfo,timestamps]=read_rdvision(FileName,num);
251    otherwise
252        errormsg=[ FileType ': invalid input file type for uvmat'];
253end
254
255%% case of image
256if ~isempty(A)
257    if strcmp(FileType,'rdvision')
258        Field.Time=timestamps;
259    end
260    if isstruct(ParamOut)
261        ParamOut.FieldName='image';
262    end
263    Npz=1;%default
264    npxy=size(A);
265    %     Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
266    %     Rangy=[npxy(1)-0.5 0.5]; %
267    Field.NbDim=2;%default
268    Field.AName='image';
269    Field.ListVarName={'Coord_y','Coord_x','A'}; %
270    if ndims(A)==3
271        if Npz==1;%color
272            Field.VarDimName={'Coord_y','Coord_x',{'Coord_y','Coord_x','rgb'}}; %
273            Field.Coord_y=[npxy(1)-0.5 0.5];
274            Field.Coord_x=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
275            if isstruct(ParamOut)
276                ParamOut.Npx=npxy(2);% display image size on the interface
277                ParamOut.Npy=npxy(1);
278            end
279%             Field.VarAttribute{3}.Mesh=1;
280        else
281            Field.NbDim=3;
282            Field.ListVarName=['AZ' Field.ListVarName];
283            Field.VarDimName={'AZ','Coord_y','Coord_x',{'AZ','Coord_y','Coord_x'}};
284            Field.AZ=[npxy(1)-0.5 0.5];
285            Field.Coord_y=[npxy(2)-0.5 0.5];
286            Field.Coord_x=[0.5 npxy(3)-0.5]; % coordinates of the first and last pixel centers
287            if isstruct(ParamOut)
288                ParamOut.Npx=npxy(3);% display image size on the interface
289                ParamOut.Npy=npxy(2);
290            end
291%             Field.VarAttribute{4}.Mesh=1;
292        end
293    else
294        Field.VarDimName={'Coord_y','Coord_x',{'Coord_y','Coord_x'}}; %
295        Field.Coord_y=[npxy(1)-0.5 0.5];
296        Field.Coord_x=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
297%        ParamOut.Npx=npxy(2);% display image size on the interface
298 %       ParamOut.Npy=npxy(1);
299%         Field.VarAttribute{3}.Mesh=1;
300    end
301    Field.A=A;
302    Field.CoordUnit='pixel'; %used for mouse_motion
303       
304end
305
306
307
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