source: trunk/src/read_field.m @ 406

Last change on this file since 406 was 406, checked in by sommeria, 12 years ago

bugs corrected in civ_matlab and object projection

File size: 9.4 KB
RevLine 
[379]1
[181]2%'read_field': read input fields in different formats
3%--------------------------------------------------------------------------
4%  function [Field,ParamOut,errormsg] = read_field(ObjectName,FileType,ParamIn)
5%
6% OUTPUT:
7% Field: matlab structure representing the field
8% ParamOut: structure representing parameters:
9%        .FieldName; field name
10%        .FieldList: menu of possible fields
11%        .VelType
12%        .CivStage: stage of civx processing (=0, not Civx, =1 (civ1), =2  (fix1)....     
13%        .Npx,.Npy: for images, nbre of pixels in x and y
14% errormsg: error message, ='' by default
15%
16%INPUT
17% ObjectName: name of the input file, or movie object when the Matlab function mmreader is used
18% FileType: type of file
19%     = netcdf : netcdf file
20%     = image : usual image as recognised by Matlab
21%     = multimage: image series stored in a single file
22%     = movie: movie read with mmreader
23%     = avi: avi movie read with aviread (OBSOLETE, used only when mmreader is not available, old versions of Matlab)
24%     = vol: images representing scanned volume (images concatened in the y direction)
25% ParamIn: Matlab structure of input parameters
26%     .FieldName: name of the input field (for Civx data)
27%     .VelType: type of velocity data ('civ1', 'filter1', 'civ2'...)
28%     .ColorVar: variable used for vector color
29%     .Npx, .Npy: nbre of pixels along x and y (used for .vol input files)
[183]30function [Field,ParamOut,errormsg] = read_field(ObjectName,FileType,ParamIn,num)
[181]31Field=[];
[354]32if ~exist('num','var')
33    num=1;
34end
35if ~exist('ParamIn','var')
36    ParamIn=[];
37end
38ParamOut=ParamIn;%default
[181]39errormsg='';
[254]40if isfield(ParamIn,'VelType')
[181]41VelType=ParamIn.VelType;
[254]42end
[334]43A=[];
44%% distingush different input file types
45switch FileType
46    case {'civx','civdata','netcdf'}  %read the first nc field
[354]47%         ParamOut.FieldName=ParamIn.FieldName;
[334]48        GUIName='get_field'; %default name of the GUI get_field
49        if isfield(ParamIn,'GUIName')
50            GUIName=ParamIn.GUIName;
51        end
[404]52        CivStage=0;
[334]53        if ~strcmp(ParamIn.FieldName,'get_field...')% if get_field is not requested, look for Civx data
54            FieldList=calc_field;%list of possible fields for Civx data
55            ParamOut.ColorVar='';%default
56            field_index=strcmp(ParamIn.FieldName,FieldList);%look for ParamIn.FieldName in the list of possible fields for Civx data
57            if isempty(find(field_index,1))% ParamIn.FieldName is not in the list, check whether Civx data exist
[380]58                Data=nc2struct(ObjectName,'ListGlobalAttribute','Conventions','absolut_time_T0','civ','CivStage');
[334]59                % case of new civdata conventions
60                if isequal(Data.Conventions,'uvmat/civdata')
61                    ParamOut.FieldName='velocity';%Civx data found, set .FieldName='velocity' by default
62                    ParamOut.ColorVar='ima_cor';
63                    InputField=[{ParamOut.FieldName} {ParamOut.ColorVar}];
[380]64                    [Field,ParamOut.VelType,errormsg]=read_civdata(ObjectName,InputField,ParamIn.VelType,Data.CivStage);
[404]65                    CivStage=Field.CivStage;
[405]66                    ParamOut.CivStage=Field.CivStage;
[334]67                    %case of old civx conventions
68                elseif ~isempty(Data.absolut_time_T0)&& ~isequal(Data.civ,0)
69                    ParamOut.FieldName='velocity';%Civx data found, set .FieldName='velocity' by default
70                    ParamOut.ColorVar='ima_cor';
71                    InputField=[{ParamOut.FieldName} {ParamOut.ColorVar}];
72                    [Field,ParamOut.VelType]=read_civxdata(ObjectName,InputField,ParamIn.VelType);
[404]73                    CivStage=Field.CivStage;
[334]74                    ParamOut.CivStage=Field.CivStage;
75                    % not cvix file, fields will be chosen through the GUI get_field
76                else
77                    ParamOut.FieldName='get_field...';
78                    hget_field=findobj(allchild(0),'Name',GUIName);%find the get_field... GUI
79                    if ~isempty(hget_field)
80                        delete(hget_field)%delete  get_field for reinitialisation
81                    end
82                end
83            else
84                InputField={ParamOut.FieldName};
85                if isfield(ParamIn,'ColorVar')
86                    ParamOut.ColorVar=ParamIn.ColorVar;
87                    InputField=[InputField {ParamOut.ColorVar}];
88                end
89                [Field,ParamOut.VelType,errormsg]=read_civxdata(ObjectName,InputField,ParamIn.VelType);
90                if ~isempty(errormsg)
91                    return
92                end
[404]93                CivStage=Field.CivStage;
[181]94                ParamOut.CivStage=Field.CivStage;
95            end
[406]96            ParamOut.FieldList=[{'image'};FieldList;{'get_field...'}];
[334]97        end
[406]98%         ParamOut.FieldList=[{'image'};FieldList;{'get_field...'}];
[404]99        if CivStage==0% read the field names on the interface get_field.
[334]100            hget_field=findobj(allchild(0),'Name',GUIName);%find the get_field... GUI
101            if isempty(hget_field)% open the GUI get_field if it is not found
102                hget_field= get_field(ObjectName);%open the get_field GUI
103                set(hget_field,'Name',GUIName)%update the name of get_field (e.g. get_field_1)
[181]104            end
[334]105            hhget_field=guidata(hget_field);
106            %% update  the get_field GUI
107            set(hhget_field.inputfile,'String',ObjectName)
108            set(hhget_field.list_fig,'Value',1)
109            if exist('num','var')&&~isnan(num)
110                set(hhget_field.TimeIndexValue,'String',num2str(num))
[236]111            end
[334]112            funct_list=get(hhget_field.ACTION,'UserData');
113            funct_index=get(hhget_field.ACTION,'Value');
114            funct=funct_list{funct_index};%select  the current action in get_field, e;g. PLOT
115            Field=funct(hget_field); %%activate the current action selected in get_field, e;g.read the names of the variables to plot
116            Tabchar={''};%default
117            Tabcell=[];
118            set(hhget_field.inputfile,'String',ObjectName)
119            if isfield(Field,'ListGlobalAttribute')&& ~isempty(Field.ListGlobalAttribute)
120                for iline=1:length(Field.ListGlobalAttribute)
121                    Tabcell{iline,1}=Field.ListGlobalAttribute{iline};
122                    if isfield(Field, Field.ListGlobalAttribute{iline})
123                        eval(['val=Field.' Field.ListGlobalAttribute{iline} ';'])
124                        if ischar(val);
125                            Tabcell{iline,2}=val;
126                        else
127                            Tabcell{iline,2}=num2str(val);
128                        end
[181]129                    end
130                end
[334]131                if ~isempty(Tabcell)
132                    Tabchar=cell2tab(Tabcell,'=');
133                    Tabchar=[{''};Tabchar];
134                end
[181]135            end
[334]136            %set(hhget_field.attributes,'String',Tabchar);%update list of global attributes in get_field
137            ParamOut.CivStage=0;
138            ParamOut.VelType=[];
139            if isfield(Field,'TimeIndex')
140                ParamOut.TimeIndex=Field.TimeIndex;
[181]141            end
[334]142            if isfield(Field,'TimeValue')
143                ParamOut.TimeValue=Field.TimeValue;
144            end
145            ParamOut.FieldList={'get_field...'};
[227]146        end
[404]147%         if CivStage~=0
148%             ParamOut.FieldList=[{'image'};FieldList;{'get_field...'}];
149%         else
150% %             ParamOut.FieldList={'get_field...'};
151%         end   
[354]152    case 'video'
[334]153        try
154            A=read(ObjectName,num);
155        catch ME
[354]156            errormsg=ME.message
[334]157            return
[227]158        end
[334]159        FieldName='image';
160    case 'vol'
161        A=imread(ObjectName);
162        Npz=size(A,1)/ParamIn.Npy;
163        A=reshape(A',ParamIn.Npx,ParamIn.Npy,Npz);
164        A=permute(A,[3 2 1]);
165        FieldName='image';
166    case 'multimage'
167        A=imread(ObjectName,num);
168        FieldName='image';
169    case 'image'
170        A=imread(ObjectName);
171        FieldName='image';
172end
173%% case of image
174if ~isempty(A)
[181]175    ParamOut.FieldName='image';
176    ParamOut.FieldList={'image'};
[182]177    Npz=1;%default
[181]178    npxy=size(A);
[397]179%     Rangx=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
180%     Rangy=[npxy(1)-0.5 0.5]; %
[181]181    Field.NbDim=2;%default
182    Field.AName='image';
183    Field.ListVarName={'AY','AX','A'}; %
184    if ndims(A)==3
185        if Npz==1;%color
186            Field.VarDimName={'AY','AX',{'AY','AX','rgb'}}; %
187            Field.AY=[npxy(1)-0.5 0.5];
188            Field.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
[182]189            ParamOut.Npx=npxy(2);% display image size on the interface
190            ParamOut.Npy=npxy(1);
[186]191            Field.VarAttribute{3}.Mesh=1;
[181]192        else
193            Field.NbDim=3;
194            Field.ListVarName=['AZ' Field.ListVarName];
195            Field.VarDimName={'AZ','AY','AX',{'AZ','AY','AX'}};
196            Field.AZ=[npxy(1)-0.5 0.5];
197            Field.AY=[npxy(2)-0.5 0.5];
198            Field.AX=[0.5 npxy(3)-0.5]; % coordinates of the first and last pixel centers
[182]199            ParamOut.Npx=npxy(3);% display image size on the interface
200            ParamOut.Npy=npxy(2);
[186]201            Field.VarAttribute{4}.Mesh=1;
[181]202        end
203    else
204        Field.VarDimName={'AY','AX',{'AY','AX'}}; %
205        Field.AY=[npxy(1)-0.5 0.5];
206        Field.AX=[0.5 npxy(2)-0.5]; % coordinates of the first and last pixel centers
[182]207        ParamOut.Npx=npxy(2);% display image size on the interface
208        ParamOut.Npy=npxy(1);
[186]209        Field.VarAttribute{3}.Mesh=1;
[181]210    end
211    Field.A=A;
212    Field.CoordUnit='pixel'; %used for mouse_motion
213end
214
215
[334]216
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