source: trunk/src/read_field.m @ 227

Last change on this file since 227 was 227, checked in by sommeria, 13 years ago

add function sub_field_series to apply the sub_field operation to a series of fileds (for instance subtracting a background to an image series)
File size: 8.3 KB
Line 
1%'read_field': read input fields in different formats
2%--------------------------------------------------------------------------
3%  function [Field,ParamOut,errormsg] = read_field(ObjectName,FileType,ParamIn)
4%
5% OUTPUT:
6% Field: matlab structure representing the field
7% ParamOut: structure representing parameters:
8%        .FieldName; field name
9%        .FieldList: menu of possible fields
10%        .VelType
11%        .CivStage: stage of civx processing (=0, not Civx, =1 (civ1), =2  (fix1)....     
12%        .Npx,.Npy: for images, nbre of pixels in x and y
13% errormsg: error message, ='' by default
14%
15%INPUT
16% ObjectName: name of the input file, or movie object when the Matlab function mmreader is used
17% FileType: type of file
18%     = netcdf : netcdf file
19%     = image : usual image as recognised by Matlab
20%     = multimage: image series stored in a single file
21%     = movie: movie read with mmreader
22%     = avi: avi movie read with aviread (OBSOLETE, used only when mmreader is not available, old versions of Matlab)
23%     = vol: images representing scanned volume (images concatened in the y direction)
24% ParamIn: Matlab structure of input parameters
25%     .FieldName: name of the input field (for Civx data)
26%     .VelType: type of velocity data ('civ1', 'filter1', 'civ2'...)
27%     .ColorVar: variable used for vector color
28%     .Npx, .Npy: nbre of pixels along x and y (used for .vol input files)
29function [Field,ParamOut,errormsg] = read_field(ObjectName,FileType,ParamIn,num)
30Field=[];
31ParamOut=[];
32errormsg='';
33VelType=ParamIn.VelType;
34
35%% case of netcdf input file
36if strcmp(FileType,'netcdf')  %read the first nc field
37    ParamOut.FieldName=ParamIn.FieldName;
38    GUIName='get_field'; %default name of the GUI getç_field
39    if isfield(ParamIn,'GUIName')
40        GUIName=ParamIn.GUIName;
41    end
42    test_civx=0;
43    ParamIn
44    if ~strcmp(ParamIn.FieldName,'get_field...')% if get_field is not requested, look for Civx data
45        FieldList=calc_field;%list of possible fields for Civx data
46        ParamOut.ColorVar='';%default
47        field_index=strcmp(ParamOut.FieldName,FieldList);%look for ParamOut.FieldName in the list
48        if isempty(find(field_index,1))% ParamOut.FieldName is not in the list, check whether Civx data exist
49            'TESTnc1'
50            Data=nc2struct(ObjectName,'ListGlobalAttribute','absolut_time_T0','civ')
51            if ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0)
52                ParamOut.FieldName='velocity';%Civx data found, set .FieldName='velocity' by default
53                ParamOut.ColorVar='ima_cor';
54                InputField=[{ParamOut.FieldName} {ParamOut.ColorVar}];
55                [Field,ParamOut.VelType]=read_civxdata(ObjectName,InputField,ParamIn.VelType);
56                test_civx=Field.CivStage;
57                ParamOut.CivStage=Field.CivStage;
58            else % not cvix file, fields will be chosen through the GUI get_field
59                ParamOut.FieldName='get_field...';
60                hget_field=findobj(allchild(0),'Name',GUIName);%find the get_field... GUI
61                if ~isempty(hget_field)
62                    delete(hget_field)%delete  get_field for reinitialisation
63                end
64            end
65        else
66            InputField={ParamOut.FieldName};
67            if isfield(ParamIn,'ColorVar')
68                ParamOut.ColorVar=ParamIn.ColorVar;
69                InputField=[InputField {ParamOut.ColorVar}];
70            end
71            [Field,ParamOut.VelType]=read_civxdata(ObjectName,InputField,ParamIn.VelType);
72            test_civx=Field.CivStage;
73            ParamOut.CivStage=Field.CivStage;
74        end
75    end
76    if ~test_civx% read the field names on the interface get_field.
77        hget_field=findobj(allchild(0),'Name',GUIName);%find the get_field... GUI
78        if isempty(hget_field)% open the GUI get_field if it is not found
79            hget_field= get_field(ObjectName);%open the get_field GUI
80            set(hget_field,'Name',GUIName)%update the name of get_field (e.g. get_field_1)
81        end
82        hhget_field=guidata(hget_field);
83        %% update  the get_field GUI
84        set(hhget_field.inputfile,'String',ObjectName)
85        set(hhget_field.list_fig,'Value',1)
86        if exist('num','var')&&~isnan(num)
87            set(hhget_field.TimeIndexValue,'String',num2str(num))
88        end
89        funct_list=get(hhget_field.ACTION,'UserData');
90        funct_index=get(hhget_field.ACTION,'Value');
91        funct=funct_list{funct_index};%select  the current action in get_field, e;g. PLOT
92        Field=funct(hget_field); %%activate the current action selected in get_field, e;g.read the names of the variables to plot
93        Tabchar={''};%default
94        Tabcell=[];
95        set(hhget_field.inputfile,'String',ObjectName)
96        if isfield(Field,'ListGlobalAttribute')&& ~isempty(Field.ListGlobalAttribute)
97            for iline=1:length(Field.ListGlobalAttribute)
98                Tabcell{iline,1}=Field.ListGlobalAttribute{iline};
99                if isfield(Field, Field.ListGlobalAttribute{iline})
100                    eval(['val=Field.' Field.ListGlobalAttribute{iline} ';'])
101                    if ischar(val);
102                        Tabcell{iline,2}=val;
103                    else
104                        Tabcell{iline,2}=num2str(val);
105                    end
106                end
107            end
108            if ~isempty(Tabcell)
109                Tabchar=cell2tab(Tabcell,'=');
110                Tabchar=[{''};Tabchar];
111            end
112        end
113        %set(hhget_field.attributes,'String',Tabchar);%update list of global attributes in get_field
114        ParamOut.CivStage=0;
115        ParamOut.VelType=[];
116        if isfield(Field,'TimeIndex')
117            ParamOut.TimeIndex=Field.TimeIndex;
118        end
119        if isfield(Field,'TimeValue')
120            ParamOut.TimeValue=Field.TimeValue;
121        end
122    end
123    if test_civx
124        ParamOut.FieldList=[{'image'};FieldList;{'get_field...'}];
125    else
126        ParamOut.FieldList={'get_field...'};
127    end
128else
129   
130    %% case of image
131    ParamOut.FieldName='image';
132    ParamOut.FieldList={'image'};
133    Npz=1;%default
134    switch FileType
135        case 'movie'
136            try
137                A=read(ObjectName,num);
138                FieldName='image';
139            catch ME
140                errormsg=ME.message;
141                return
142            end
143        case 'avi'
144            try
145                mov=aviread(ObjectName,num);
146            catch ME
147                errormsg=ME.message;
148                return
149            end
150            A=frame2im(mov(1));
151            FieldName='image';
152        case 'vol'
153            A=imread(ObjectName);
154            Npz=size(A,1)/ParamIn.Npy;
155            A=reshape(A',ParamIn.Npx,ParamIn.Npy,Npz);
156            A=permute(A,[3 2 1]);
157            FieldName='image';
158        case 'multimage'
159            A=imread(ObjectName,num);
160            FieldName='image';
161        case 'image'
162            A=imread(ObjectName);
163            FieldName='image';
164    end
165    npxy=size(A);
166    Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
167    Rangy=[npxy(1)-0.5 0.5]; %
168    Field.NbDim=2;%default
169    Field.AName='image';
170    Field.ListVarName={'AY','AX','A'}; %
171    if ndims(A)==3
172        if Npz==1;%color
173            Field.VarDimName={'AY','AX',{'AY','AX','rgb'}}; %
174            Field.AY=[npxy(1)-0.5 0.5];
175            Field.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
176            ParamOut.Npx=npxy(2);% display image size on the interface
177            ParamOut.Npy=npxy(1);
178            Field.VarAttribute{3}.Mesh=1;
179        else
180            Field.NbDim=3;
181            Field.ListVarName=['AZ' Field.ListVarName];
182            Field.VarDimName={'AZ','AY','AX',{'AZ','AY','AX'}};
183            Field.AZ=[npxy(1)-0.5 0.5];
184            Field.AY=[npxy(2)-0.5 0.5];
185            Field.AX=[0.5 npxy(3)-0.5]; % coordinates of the first and last pixel centers
186            ParamOut.Npx=npxy(3);% display image size on the interface
187            ParamOut.Npy=npxy(2);
188            Field.VarAttribute{4}.Mesh=1;
189        end
190    else
191        Field.VarDimName={'AY','AX',{'AY','AX'}}; %
192        Field.AY=[npxy(1)-0.5 0.5];
193        Field.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
194        ParamOut.Npx=npxy(2);% display image size on the interface
195        ParamOut.Npy=npxy(1);
196        Field.VarAttribute{3}.Mesh=1;
197    end
198    Field.A=A;
199    Field.CoordUnit='pixel'; %used for mouse_motion
200end
201
202
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