source: trunk/src/read_field.m @ 675

Last change on this file since 675 was 675, checked in by sommeria, 11 years ago

various bugs corrected

File size: 7.8 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_type.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% num: frame number for movies
23%
24% see also read_image.m,read_civxdata.m,read_civdata.m,
25
26function [Field,ParamOut,errormsg] = read_field(FileName,FileType,ParamIn,num)
27Field=[];
28if ~exist('num','var')
29    num=1;
30end
31if ~exist('ParamIn','var')
32    ParamIn=[];
33end
34ParamOut=ParamIn;%default
35errormsg='';
36if ~exist(FileName,'file')
37    erromsg=['input file ' FileName ' does not exist'];
38    return
39end
40A=[];
41InputField={};
42check_colorvar=0;
43if isstruct(ParamIn)
44    if isfield(ParamIn,'FieldName')
45        if ischar(ParamIn.FieldName)
46            InputField={ParamIn.FieldName};
47        else
48            InputField= ParamIn.FieldName;
49        end
50    end
51    check_colorvar=zeros(size(InputField));
52    if isfield(ParamIn,'ColorVar')
53        InputField=[ParamIn.FieldName {ParamIn.ColorVar}];
54        check_colorvar(numel(InputField))=1;
55    end
56end
57
58%% distingush different input file types
59switch FileType
60    case 'civdata'
61        [Field,ParamOut.VelType,errormsg]=read_civdata(FileName,InputField,ParamIn.VelType);
62        if ~isempty(errormsg),errormsg=['read_civdata / ' errormsg];return,end
63        ParamOut.CivStage=Field.CivStage;
64    case 'civx'
65        ParamOut.FieldName='velocity';%Civx data found, set .FieldName='velocity' by default
66        [Field,ParamOut.VelType,errormsg]=read_civxdata(FileName,InputField,ParamIn.VelType);
67        if ~isempty(errormsg),errormsg=['read_civxdata / ' errormsg];return,end
68        ParamOut.CivStage=Field.CivStage;
69    case 'netcdf'
70        ListVar={};
71        Role={};
72        ProjModeRequest={};
73        for ilist=1:numel(InputField)
74            r=regexp(InputField{ilist},'(?<Operator>(^vec|^norm))\((?<UName>.+),(?<VName>.+)\)$','names');
75            if isempty(r)%  no operator used
76                ListVar=[ListVar InputField(ilist)];
77                if check_colorvar(ilist)
78                    Role{numel(ListVar)}='ancillary';% not projected with interpolation
79                    ProjModeRequest{numel(ListVar)}='';
80                else
81                    Role{numel(ListVar)}='scalar';
82                    ProjModeRequest{numel(ListVar)}='interp_lin';%scalar field (requires interpolation for plot)
83                end
84            else  % an operator 'vec' or 'norm' is used
85                if ~check_colorvar(ilist) && strcmp(r.Operator,'norm')
86                    ProjModeRequestVar='interp_lin';%scalar field (requires interpolation for plot)
87                else
88                    ProjModeRequestVar='';
89                end
90                ind_var_U=find(strcmp(r.UName,ListVar));%check previous listing of variable r.UName
91                ind_var_V=find(strcmp(r.VName,ListVar));%check previous listing of variable r.VName
92                if isempty(ind_var_U)
93                    ListVar=[ListVar r.UName]; % append the variable in the list if not previously listed
94                    Role=[Role {'vector_x'}];
95                    ProjModeRequest=[ProjModeRequest {ProjModeRequestVar}];
96                end
97                if isempty(ind_var_V)
98                    ListVar=[ListVar r.VName];% append the variable in the list if not previously listed
99                    Role=[Role {'vector_y'}];
100                    ProjModeRequest=[ProjModeRequest {ProjModeRequestVar}];
101                end
102            end
103        end
104        if isfield(ParamIn,'TimeDimName')% case of reading of a single time index in a multidimensional array
105            [Field,var_detect,ichoice]=nc2struct(FileName,'TimeDimName',ParamIn.TimeDimName,num,[ParamIn.Coord_x (ParamIn.Coord_y) ListVar]);
106        else
107            [Field,var_detect,ichoice]=nc2struct(FileName,[ParamIn.Coord_x (ParamIn.Coord_y) ListVar]);
108        end
109        if isfield(Field,'Txt')
110            errormsg=Field.Txt;
111            return
112        end
113        for ilist=3:numel(Field.VarDimName)
114            if isequal(Field.VarDimName{1},Field.VarDimName{ilist})
115                Field.VarAttribute{1}.Role='coord_x';%unstructured coordinates
116                Field.VarAttribute{2}.Role='coord_y';
117                break
118            end
119        end
120        for ivar=1:numel(ListVar)
121            Field.VarAttribute{ivar+2}.Role=Role{ivar};
122            if isfield(ParamIn,'FieldName')
123                Field.VarAttribute{ivar+2}.FieldName=ParamIn.FieldName;
124            end
125            Field.VarAttribute{ivar+2}.ProjModeRequest=ProjModeRequest{ivar};
126        end
127
128    case 'video'
129        if strcmp(class(ParamIn),'VideoReader')
130            A=read(ParamIn,num);
131        else
132            ParamOut=VideoReader(FileName);
133            A=read(ParamOut,num);
134        end
135    case 'mmreader'
136        if strcmp(class(ParamIn),'mmreader')
137            A=read(ParamIn,num);
138        else
139            ParamOut=mmreader(FileName);
140            A=read(ParamOut,num);
141        end
142    case 'vol'
143        A=imread(FileName);
144        Npz=size(A,1)/ParamIn.Npy;
145        A=reshape(A',ParamIn.Npx,ParamIn.Npy,Npz);
146        A=permute(A,[3 2 1]);
147    case 'multimage'
148        warning 'off'
149        A=imread(FileName,num);
150    case 'image'
151        A=imread(FileName);
152end
153if ~isempty(errormsg)
154    errormsg=[FileType ' input: ' errormsg];
155    return
156end
157
158%% case of image
159if ~isempty(A)
160    if isstruct(ParamOut)
161        ParamOut.FieldName='image';
162    end
163    Npz=1;%default
164    npxy=size(A);
165    %     Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
166    %     Rangy=[npxy(1)-0.5 0.5]; %
167    Field.NbDim=2;%default
168    Field.AName='image';
169    Field.ListVarName={'AY','AX','A'}; %
170    if ndims(A)==3
171        if Npz==1;%color
172            Field.VarDimName={'AY','AX',{'AY','AX','rgb'}}; %
173            Field.AY=[npxy(1)-0.5 0.5];
174            Field.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
175            if isstruct(ParamOut)
176                ParamOut.Npx=npxy(2);% display image size on the interface
177                ParamOut.Npy=npxy(1);
178            end
179            Field.VarAttribute{3}.Mesh=1;
180        else
181            Field.NbDim=3;
182            Field.ListVarName=['AZ' Field.ListVarName];
183            Field.VarDimName={'AZ','AY','AX',{'AZ','AY','AX'}};
184            Field.AZ=[npxy(1)-0.5 0.5];
185            Field.AY=[npxy(2)-0.5 0.5];
186            Field.AX=[0.5 npxy(3)-0.5]; % coordinates of the first and last pixel centers
187            if isstruct(ParamOut)
188                ParamOut.Npx=npxy(3);% display image size on the interface
189                ParamOut.Npy=npxy(2);
190            end
191            Field.VarAttribute{4}.Mesh=1;
192        end
193    else
194        Field.VarDimName={'AY','AX',{'AY','AX'}}; %
195        Field.AY=[npxy(1)-0.5 0.5];
196        Field.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
197        ParamOut.Npx=npxy(2);% display image size on the interface
198        ParamOut.Npy=npxy(1);
199        Field.VarAttribute{3}.Mesh=1;
200    end
201    Field.A=A;
202    Field.CoordUnit='pixel'; %used for mouse_motion
203end
204
205
206
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