source: trunk/src/read_field.m @ 887

Last change on this file since 887 was 880, checked in by sommeria, 9 years ago

various bug fixes

File size: 12.8 KB
RevLine 
[497]1%'read_field': read the fields from files in different formats (netcdf files, images, video)
[181]2%--------------------------------------------------------------------------
[450]3%  function [Field,ParamOut,errormsg] = read_field(FileName,FileType,ParamIn,num)
[181]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
[466]15% FileName: name of the input file
[784]16% FileType: type of file, as determined by the function get_file_info.m
[450]17% ParamIn: movie object or Matlab structure of input parameters
[445]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'...)
[181]20%     .ColorVar: variable used for vector color
21%     .Npx, .Npy: nbre of pixels along x and y (used for .vol input files)
[693]22%     .TimeDimName: name of the dimension considered as 'time', selected index value then set by input 'num'   
[466]23% num: frame number for movies
[497]24%
25% see also read_image.m,read_civxdata.m,read_civdata.m,
[466]26
[809]27%=======================================================================
28% Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF 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
[450]45function [Field,ParamOut,errormsg] = read_field(FileName,FileType,ParamIn,num)
[748]46%% default output and check input
[181]47Field=[];
[354]48if ~exist('num','var')
49    num=1;
50end
51if ~exist('ParamIn','var')
52    ParamIn=[];
53end
54ParamOut=ParamIn;%default
[181]55errormsg='';
[635]56if ~exist(FileName,'file')
[747]57    errormsg=['input file ' FileName ' does not exist'];
[635]58    return
59end
[334]60A=[];
[575]61InputField={};
62check_colorvar=0;
[526]63if isstruct(ParamIn)
[575]64    if isfield(ParamIn,'FieldName')
65        if ischar(ParamIn.FieldName)
[576]66            InputField={ParamIn.FieldName};
[575]67        else
68            InputField= ParamIn.FieldName;
69        end
[526]70    end
[654]71    check_colorvar=zeros(size(InputField));
[684]72    if isfield(ParamIn,'ColorVar')&&~isempty(ParamIn.ColorVar)
[526]73        InputField=[ParamIn.FieldName {ParamIn.ColorVar}];
[654]74        check_colorvar(numel(InputField))=1;
[526]75    end
[521]76end
[575]77
[334]78%% distingush different input file types
[527]79switch FileType
[748]80    case 'civdata'% new format for civ results
[527]81        [Field,ParamOut.VelType,errormsg]=read_civdata(FileName,InputField,ParamIn.VelType);
82        if ~isempty(errormsg),errormsg=['read_civdata / ' errormsg];return,end
[822]83%         if ~isempty(strcmp('C',ParamIn.FieldName))% if C image correlation is requested as field (not color visu)
84%             ScalarIndex=strcmp('C',Field.ListVarName);
85%             Field.VarAttribute{ScalarIndex}.Role='scalar';%put role as 'scalar' instead of ancillary
86%         end     
[527]87        ParamOut.CivStage=Field.CivStage;
[748]88    case 'civx'% old (obsolete) format for civ results
[527]89        ParamOut.FieldName='velocity';%Civx data found, set .FieldName='velocity' by default
90        [Field,ParamOut.VelType,errormsg]=read_civxdata(FileName,InputField,ParamIn.VelType);
91        if ~isempty(errormsg),errormsg=['read_civxdata / ' errormsg];return,end
92        ParamOut.CivStage=Field.CivStage;
[748]93    case 'netcdf'% general netcdf file (not recognized as civ)
[527]94        ListVar={};
[675]95        Role={};
96        ProjModeRequest={};
[684]97        ListInputField={};
98        ListOperator={};
[681]99        checkU=0;
100        checkV=0;
[527]101        for ilist=1:numel(InputField)
[748]102            % look for input variables to read
[527]103            r=regexp(InputField{ilist},'(?<Operator>(^vec|^norm))\((?<UName>.+),(?<VName>.+)\)$','names');
[654]104            if isempty(r)%  no operator used
[681]105                if isempty(find(strcmp(InputField{ilist},ListVar)))
[684]106                    ListVar=[ListVar InputField(ilist)];%append the variable name if not already in the list
107                    ListInputField=[ListInputField InputField(ilist)];
108                    ListOperator=[ListOperator {''}];
[681]109                end
[654]110                if check_colorvar(ilist)
[667]111                    Role{numel(ListVar)}='ancillary';% not projected with interpolation
112                    ProjModeRequest{numel(ListVar)}='';
[654]113                else
[667]114                    Role{numel(ListVar)}='scalar';
115                    ProjModeRequest{numel(ListVar)}='interp_lin';%scalar field (requires interpolation for plot)
[654]116                end
117            else  % an operator 'vec' or 'norm' is used
[667]118                if ~check_colorvar(ilist) && strcmp(r.Operator,'norm')
[675]119                    ProjModeRequestVar='interp_lin';%scalar field (requires interpolation for plot)
[667]120                else
[675]121                    ProjModeRequestVar='';
[667]122                end
[675]123                ind_var_U=find(strcmp(r.UName,ListVar));%check previous listing of variable r.UName
124                ind_var_V=find(strcmp(r.VName,ListVar));%check previous listing of variable r.VName
125                if isempty(ind_var_U)
[684]126                    ListVar=[ListVar {r.UName}]; % append the variable in the list if not previously listed
[675]127                    Role=[Role {'vector_x'}];
128                    ProjModeRequest=[ProjModeRequest {ProjModeRequestVar}];
[684]129                    ListInputField=[ListInputField InputField(ilist)];
130                    %ListOperator=[ListOperator {[r.Operator '_U']}];
[681]131                else
132                    checkU=1;
[675]133                end
134                if isempty(ind_var_V)
[684]135                    ListVar=[ListVar {r.VName}];% append the variable in the list if not previously listed
[675]136                    Role=[Role {'vector_y'}];
137                    ProjModeRequest=[ProjModeRequest {ProjModeRequestVar}];
[867]138                    ListInputField=[ListInputField InputField(ilist)];
139                    %ListInputField=[ListInputField {''}];
[681]140                else
141                    checkV=1;
[675]142                end
[493]143            end
[527]144        end
[748]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);
[648]149        if isfield(ParamIn,'TimeDimName')% case of reading of a single time index in a multidimensional array
[748]150            [Field,var_detect,ichoice,errormsg]=nc2struct(FileName,'TimeDimName',ParamIn.TimeDimName,num,[ParamIn.Coord_x ParamIn.Coord_y ParamIn.Coord_z ListVar]);
[747]151        elseif isfield(ParamIn,'TimeVarName')% case of reading of a single time  in a multidimensional array
[748]152            [Field,var_detect,ichoice,errormsg]=nc2struct(FileName,'TimeVarName',ParamIn.TimeVarName,num,[ParamIn.Coord_x ParamIn.Coord_y ParamIn.Coord_z ListVar]);
153            NbCoord=NbCoord+1;% adds time coordinate
[648]154        else
[748]155            [Field,var_detect,ichoice,errormsg]=nc2struct(FileName,[ParamIn.Coord_x ParamIn.Coord_y ParamIn.Coord_z ListVar]);
[648]156        end
[747]157        if ~isempty(errormsg)
[534]158            return
159        end
[748]160        %scan all the variables beyond the two first ones, ParamIn.Coord_x and ParamIn.Coord_y.
161        for ilist=NbCoord+1:numel(Field.VarDimName)
162            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
[675]163                Field.VarAttribute{1}.Role='coord_x';%unstructured coordinates
164                Field.VarAttribute{2}.Role='coord_y';
[748]165                if NbCoord>=3
166                    Field.VarAttribute{3}.Role='coord_z';
167                end
[675]168                break
169            end
170        end
[684]171        NormName='';
172        UName='';
173        VName='';
174        for ilist=1:numel(ListVar)
[748]175            Field.VarAttribute{ilist+NbCoord}.Role=Role{ilist};
176            Field.VarAttribute{ilist+NbCoord}.ProjModeRequest=ProjModeRequest{ilist};
[648]177            if isfield(ParamIn,'FieldName')
[748]178                Field.VarAttribute{ilist+NbCoord}.FieldName=ListInputField{ilist};
[648]179            end
[684]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;
[681]194            end
195        end
[684]196        if ~isempty(NormName)% remove U and V if norm has been calculated and U and V are not needed as variables
197            ind_var_U=find(strcmp(UName,ListVar));%check previous listing of variable r.UName
198            ind_var_V=find(strcmp(VName,ListVar));%check previous listing of variable r.VName
[769]199            if ~checkU && ~checkV
200                Field.ListVarName([ind_var_U+2 ind_var_V+2])=[];
201                Field.VarDimName([ind_var_U+2 ind_var_V+2])=[];
202                Field.VarAttribute([ind_var_U+2 ind_var_V+2])=[];
203            elseif ~checkU
204                Field.ListVarName(ind_var_U+2)=[];
205                Field.VarDimName(ind_var_U+2)=[];
206                Field.VarAttribute(ind_var_U+2 )=[];
207            elseif ~checkV
208                Field.ListVarName(ind_var_V+2)=[];
209                Field.VarDimName(ind_var_V+2)=[];
210                Field.VarAttribute(ind_var_V+2 )=[];
211            end
[684]212        end
[527]213    case 'video'
214        if strcmp(class(ParamIn),'VideoReader')
215            A=read(ParamIn,num);
216        else
217            ParamOut=VideoReader(FileName);
218            A=read(ParamOut,num);
219        end
220    case 'mmreader'
221        if strcmp(class(ParamIn),'mmreader')
222            A=read(ParamIn,num);
223        else
224            ParamOut=mmreader(FileName);
225            A=read(ParamOut,num);
226        end
227    case 'vol'
228        A=imread(FileName);
229        Npz=size(A,1)/ParamIn.Npy;
230        A=reshape(A',ParamIn.Npx,ParamIn.Npy,Npz);
231        A=permute(A,[3 2 1]);
232    case 'multimage'
[784]233      %  warning 'off'
[527]234        A=imread(FileName,num);
235    case 'image'
236        A=imread(FileName);
[784]237    case 'rdvision'
[785]238        [A,FileInfo,timestamps]=read_rdvision(FileName,num);
[784]239    otherwise
240        errormsg=[ FileType ': invalid input file type for uvmat'];
[527]241end
[445]242
[334]243%% case of image
244if ~isempty(A)
[784]245    if strcmp(FileType,'rdvision')
246        Field.Time=timestamps;
247    end
[452]248    if isstruct(ParamOut)
[580]249        ParamOut.FieldName='image';
[452]250    end
[182]251    Npz=1;%default
[181]252    npxy=size(A);
[580]253    %     Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
254    %     Rangy=[npxy(1)-0.5 0.5]; %
[181]255    Field.NbDim=2;%default
256    Field.AName='image';
[782]257    Field.ListVarName={'Coord_y','Coord_x','A'}; %
[181]258    if ndims(A)==3
259        if Npz==1;%color
[782]260            Field.VarDimName={'Coord_y','Coord_x',{'Coord_y','Coord_x','rgb'}}; %
261            Field.Coord_y=[npxy(1)-0.5 0.5];
262            Field.Coord_x=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
[452]263            if isstruct(ParamOut)
[580]264                ParamOut.Npx=npxy(2);% display image size on the interface
265                ParamOut.Npy=npxy(1);
[452]266            end
[871]267%             Field.VarAttribute{3}.Mesh=1;
[181]268        else
269            Field.NbDim=3;
270            Field.ListVarName=['AZ' Field.ListVarName];
[782]271            Field.VarDimName={'AZ','Coord_y','Coord_x',{'AZ','Coord_y','Coord_x'}};
[181]272            Field.AZ=[npxy(1)-0.5 0.5];
[782]273            Field.Coord_y=[npxy(2)-0.5 0.5];
274            Field.Coord_x=[0.5 npxy(3)-0.5]; % coordinates of the first and last pixel centers
[452]275            if isstruct(ParamOut)
[580]276                ParamOut.Npx=npxy(3);% display image size on the interface
277                ParamOut.Npy=npxy(2);
278            end
[871]279%             Field.VarAttribute{4}.Mesh=1;
[181]280        end
281    else
[782]282        Field.VarDimName={'Coord_y','Coord_x',{'Coord_y','Coord_x'}}; %
283        Field.Coord_y=[npxy(1)-0.5 0.5];
284        Field.Coord_x=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
[880]285%        ParamOut.Npx=npxy(2);% display image size on the interface
286 %       ParamOut.Npy=npxy(1);
[871]287%         Field.VarAttribute{3}.Mesh=1;
[181]288    end
289    Field.A=A;
290    Field.CoordUnit='pixel'; %used for mouse_motion
[784]291       
[181]292end
293
294
[334]295
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