source: trunk/src/read_field.m @ 1007

Last change on this file since 1007 was 1007, checked in by sommeria, 4 years ago

functions to read DaVis? images added

File size: 14.6 KB
Line 
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 2008-2017, 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 'pivdata_fluidimage'
85        [Field,ParamOut.VelType,errormsg]=read_pivdata_fluidimage(FileName,InputField,ParamIn.VelType);
86        ParamOut.CivStage=Field.CivStage;
87    case 'civx'% old (obsolete) format for civ results
88        ParamOut.FieldName='velocity';%Civx data found, set .FieldName='velocity' by default
89        [Field,ParamOut.VelType,errormsg]=read_civxdata(FileName,InputField,ParamIn.VelType);
90        if ~isempty(errormsg),errormsg=['read_civxdata / ' errormsg];return,end
91        ParamOut.CivStage=Field.CivStage;
92    case 'netcdf'% general netcdf file (not recognized as civ)
93        ListVar={};
94        Role={};
95        ProjModeRequest={};
96        ListInputField={};
97        ListOperator={};
98        checkU=0;
99        checkV=0;
100        for ilist=1:numel(InputField)
101            % look for input variables to read
102            r=regexp(InputField{ilist},'(?<Operator>(^vec|^norm))\((?<UName>.+),(?<VName>.+)\)$','names');
103            if isempty(r)%  no operator used
104                if isempty(find(strcmp(InputField{ilist},ListVar)))
105                    ListVar=[ListVar InputField(ilist)];%append the variable name if not already in the list
106                    ListInputField=[ListInputField InputField(ilist)];
107                    ListOperator=[ListOperator {''}];
108                end
109                if check_colorvar(ilist)
110                    if isempty(find(strcmp(InputField{ilist},ListVar)))
111                    Role{numel(ListVar)}='ancillary';% not projected with interpolation
112                    ProjModeRequest{numel(ListVar)}='';
113                    end
114                else
115                    Role{numel(ListVar)}='scalar';
116                    ProjModeRequest{numel(ListVar)}='interp_lin';%scalar field (requires interpolation for plot)
117                end
118            else  % an operator 'vec' or 'norm' is used
119                if ~check_colorvar(ilist) && strcmp(r.Operator,'norm')
120                    ProjModeRequestVar='interp_lin';%scalar field (requires interpolation for plot)
121                else
122                    ProjModeRequestVar='';
123                end
124                ind_var_U=find(strcmp(r.UName,ListVar));%check previous listing of variable r.UName
125                ind_var_V=find(strcmp(r.VName,ListVar));%check previous listing of variable r.VName
126                if isempty(ind_var_U)
127                    ListVar=[ListVar {r.UName}]; % append the variable in the list if not previously listed
128                    Role=[Role {'vector_x'}];
129                    ProjModeRequest=[ProjModeRequest {ProjModeRequestVar}];
130                    ListInputField=[ListInputField InputField(ilist)];
131                else
132                    checkU=1;
133                end
134                if isempty(ind_var_V)
135                    ListVar=[ListVar {r.VName}];% append the variable in the list if not previously listed
136                    Role=[Role {'vector_y'}];
137                    ProjModeRequest=[ProjModeRequest {ProjModeRequestVar}];
138                    ListInputField=[ListInputField InputField(ilist)];
139                   
140                else
141                    checkV=1;
142                end
143            end
144        end
145        if ~isfield(ParamIn,'Coord_z')
146            ParamIn.Coord_z=[];
147        end
148        NbCoord=~isempty(ParamIn.Coord_x)+~isempty(ParamIn.Coord_y)+~isempty(ParamIn.Coord_z);
149        if isfield(ParamIn,'TimeDimName')% case of reading of a single time index in a multidimensional array
150            [Field,var_detect,ichoice,errormsg]=nc2struct(FileName,'TimeDimName',ParamIn.TimeDimName,num,[ParamIn.Coord_x ParamIn.Coord_y ParamIn.Coord_z ListVar]);
151        elseif isfield(ParamIn,'TimeVarName')% case of reading of a single time  in a multidimensional array
152            [Field,var_detect,ichoice,errormsg]=nc2struct(FileName,'TimeVarName',ParamIn.TimeVarName,num,[ParamIn.Coord_x ParamIn.Coord_y ParamIn.Coord_z ListVar]);
153            if numel(num)~=1
154                NbCoord=NbCoord+1;% adds time coordinate, except if a single time has been selected
155            end
156        else
157            [Field,var_detect,ichoice,errormsg]=nc2struct(FileName,[ParamIn.Coord_x ParamIn.Coord_y ParamIn.Coord_z ListVar]);
158        end
159        if ~isempty(errormsg)
160            return
161        end
162        CheckStructured=1;
163        %scan all the variables beyond the two first NbCoord ones describing the coordinates.
164        for ilist=NbCoord+1:numel(Field.VarDimName)
165            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
166                Field.VarAttribute{1}.Role='coord_x';%unstructured coordinates
167                Field.VarAttribute{2}.Role='coord_y';
168                if NbCoord>=3
169                    Field.VarAttribute{3}.Role='coord_z';
170                end
171                CheckUnstructured=0;
172                break
173            end
174        end
175        if CheckStructured
176            for ilist=NbCoord+1:numel(Field.VarDimName)
177                if numel(Field.VarDimName{ilist})==NbCoord
178                    rank(1)=find(strcmp(ParamIn.Coord_x,Field.VarDimName{ilist}));
179                    rank(2)=find(strcmp(ParamIn.Coord_y,Field.VarDimName{ilist}));
180                    if NbCoord==3
181                        rank(3)=find(strcmp(ParamIn.Coord_z,Field.VarDimName{ilist}));
182                    end
183                    rank=rank(end:-1:1);
184                    VarName=Field.ListVarName{ilist};
185                    Field.(VarName)=permute(Field.(VarName),rank);
186                    Field.VarDimName{ilist}=Field.VarDimName{ilist}(rank);% permute the order of dimensions
187                end
188            end
189        end
190        NormName='';
191        UName='';
192        VName='';
193        if numel(Field.ListVarName)>NbCoord % if there are variables beyond coord (1 D plots)
194            for ilist=1:numel(ListVar)
195                Field.VarAttribute{ilist+NbCoord}.Role=Role{ilist};
196                Field.VarAttribute{ilist+NbCoord}.ProjModeRequest=ProjModeRequest{ilist};
197                if isfield(ParamIn,'FieldName')
198                    Field.VarAttribute{ilist+NbCoord}.FieldName=ListInputField{ilist};
199                end
200                r=regexp(ListInputField{ilist},'(?<Operator>(^vec|^norm))\((?<UName>.+),(?<VName>.+)\)$','names');
201                if ~isempty(r)&& strcmp(r.Operator,'norm')
202                    NormName='norm';
203                    if ~isempty(find(strcmp(ListVar,'norm')))
204                        NormName='norm_1';
205                    end
206                    Field.ListVarName=[Field.ListVarName {NormName}];
207                    ilistmax=numel(Field.ListVarName);
208                    Field.VarDimName{ilistmax}=Field.VarDimName{ilist+2};
209                    Field.VarAttribute{ilistmax}.Role='scalar';
210                    Field.(NormName)=Field.(r.UName).*Field.(r.UName)+Field.(r.VName).*Field.(r.VName);
211                    Field.(NormName)=sqrt(Field.(NormName));
212                    UName=r.UName;
213                    VName=r.VName;
214                end
215            end
216           
217            if ~isempty(NormName)% remove U and V if norm has been calculated and U and V are not needed as variables
218                ind_var_U=find(strcmp(UName,ListVar));%check previous listing of variable r.UName
219                ind_var_V=find(strcmp(VName,ListVar));%check previous listing of variable r.VName
220                if ~checkU && ~checkV
221                    Field.ListVarName([ind_var_U+2 ind_var_V+2])=[];
222                    Field.VarDimName([ind_var_U+2 ind_var_V+2])=[];
223                    Field.VarAttribute([ind_var_U+2 ind_var_V+2])=[];
224                elseif ~checkU
225                    Field.ListVarName(ind_var_U+2)=[];
226                    Field.VarDimName(ind_var_U+2)=[];
227                    Field.VarAttribute(ind_var_U+2 )=[];
228                elseif ~checkV
229                    Field.ListVarName(ind_var_V+2)=[];
230                    Field.VarDimName(ind_var_V+2)=[];
231                    Field.VarAttribute(ind_var_V+2 )=[];
232                end
233            end
234            % insert coordinates as indices in case of plots vs matrix index
235            if isfield(ParamIn,'CheckCoordIndex') && ParamIn.CheckCoordIndex
236                Field.ListVarName=[Field.ListDimName Field.ListVarName];
237                Field.VarDimName=[Field.ListDimName Field.VarDimName];
238                for idim=1:numel(Field.ListDimName)
239                    CoordName=Field.ListDimName{idim};
240                    Field.(CoordName)=1:Field.DimValue(idim);
241                end
242                Field.VarAttribute=[cell(1,numel(Field.ListDimName)) Field.VarAttribute];
243            end
244           
245        end
246    case 'video'
247        if strcmp(class(ParamIn),'VideoReader')
248            A=read(ParamIn,num);
249        else
250            ParamOut=VideoReader(FileName);
251            A=read(ParamOut,num);
252        end
253    case 'mmreader'
254        if strcmp(class(ParamIn),'mmreader')
255            A=read(ParamIn,num);
256        else
257            ParamOut=mmreader(FileName);
258            A=read(ParamOut,num);
259        end
260    case 'vol'
261        A=imread(FileName);
262        Npz=size(A,1)/ParamIn.Npy;
263        A=reshape(A',ParamIn.Npx,ParamIn.Npy,Npz);
264        A=permute(A,[3 2 1]);
265    case 'multimage'
266        %  warning 'off'
267        A=imread(FileName,num);
268    case 'image'
269        A=imread(FileName);
270    case 'rdvision'
271        [A,FileInfo,timestamps]=read_rdvision(FileName,num);
272    case 'image_DaVis'
273        Input=readimx(FileName);
274        A=Input.Frames{num}.Components{1}.Planes{1}';
275    case 'cine_phantom'
276        [A,FileInfo] = read_cine_phantom(FileName,num );
277    otherwise
278        errormsg=[ FileType ': invalid input file type for uvmat'];
279end
280
281%% case of image
282if ~isempty(A)
283    if strcmp(FileType,'rdvision')
284        Field.Time=timestamps;
285    end
286    if isstruct(ParamOut)
287        ParamOut.FieldName='image';
288    end
289    Npz=1;%default
290    npxy=size(A);
291    %     Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
292    %     Rangy=[npxy(1)-0.5 0.5]; %
293    Field.NbDim=2;%default
294    Field.AName='image';
295    Field.ListVarName={'Coord_y','Coord_x','A'}; %
296    if ndims(A)==3
297        if Npz==1;%color
298            Field.VarDimName={'Coord_y','Coord_x',{'Coord_y','Coord_x','rgb'}}; %
299            Field.Coord_y=[npxy(1)-0.5 0.5];
300            Field.Coord_x=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
301            if isstruct(ParamOut)
302                ParamOut.Npx=npxy(2);% display image size on the interface
303                ParamOut.Npy=npxy(1);
304            end
305%             Field.VarAttribute{3}.Mesh=1;
306        else
307            Field.NbDim=3;
308            Field.ListVarName=['AZ' Field.ListVarName];
309            Field.VarDimName={'AZ','Coord_y','Coord_x',{'AZ','Coord_y','Coord_x'}};
310            Field.AZ=[npxy(1)-0.5 0.5];
311            Field.Coord_y=[npxy(2)-0.5 0.5];
312            Field.Coord_x=[0.5 npxy(3)-0.5]; % coordinates of the first and last pixel centers
313            if isstruct(ParamOut)
314                ParamOut.Npx=npxy(3);% display image size on the interface
315                ParamOut.Npy=npxy(2);
316            end
317%             Field.VarAttribute{4}.Mesh=1;
318        end
319    else
320        Field.VarDimName={'Coord_y','Coord_x',{'Coord_y','Coord_x'}}; %
321        Field.Coord_y=[npxy(1)-0.5 0.5];
322        Field.Coord_x=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
323%        ParamOut.Npx=npxy(2);% display image size on the interface
324 %       ParamOut.Npy=npxy(1);
325%         Field.VarAttribute{3}.Mesh=1;
326    end
327    Field.A=A;
328    Field.CoordUnit='pixel'; %used for mouse_motion
329       
330end
331
332
333
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