source: trunk/src/read_civdata.m @ 501

Last change on this file since 501 was 497, checked in by sommeria, 9 years ago

cleaning and small bug repair.
pb of histogram for filter data solved
display of uicontrol by right mouse selection improved

File size: 8.4 KB
Line 
1%'read_civdata': reads new civ data from netcdf files
2%------------------------------------------------------------------
3%
4% function [Field,VelTypeOut]=read_civxdata(filename,FieldNames,VelType)
5%
6% OUTPUT:
7% Field: structure representing the selected field, containing
8%            .Txt: (char string) error message if any
9%            .ListGlobalAttribute: list of global attributes containing:
10%                    .NbCoord: number of vector components
11%                    .NbDim: number of dimensions (=2 or 3)
12%                    .dt: time interval for the corresponding image pair
13%                    .Time: absolute time (average of the initial image pair)
14%                    .CivStage: =0,
15%                       =1, civ1 has been performed only
16%                       =2, fix1 has been performed
17%                       =3, pacth1 has been performed
18%                       =4, civ2 has been performed
19%                       =5, fix2 has been performed
20%                       =6, pacth2 has been performed
21%                     .CoordUnit: 'pixel'
22%             .ListVarName: {'X'  'Y'  'U'  'V'  'F'  'FF'}
23%                   .X, .Y, .Z: set of vector coordinates
24%                    .U,.V,.W: corresponding set of vector components
25%                    .F: warning flags
26%                    .FF: error flag, =0 for good vectors
27%                     .C: scalar associated with velocity (used for vector colors)
28%                    .DijU; matrix of spatial derivatives (DijU(1,1,:)=DUDX,
29%                        DijU(1,2,:)=DUDY, Dij(2,1,:)=DVDX, DijU(2,2,:)=DVDY
30%
31% VelTypeOut: velocity type corresponding to the selected field: ='civ1','interp1','interp2','civ2'....
32%
33% INPUT:
34% filename: file name (string).
35% FieldNames =cell of field names to get, which can contain the strings:
36%             'ima_cor': image correlation, vec_c or vec2_C
37%             'vort','div','strain': requires velocity derivatives DUDX...
38%             'error': error estimate (vec_E or vec2_E)
39%             
40% VelType : character string indicating the types of velocity fields to read ('civ1','civ2'...)
41%            if vel_type=[] or'*', a  priority choice, given by vel_type_out{1,2}, is done depending
42%            if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1)
43
44
45% FUNCTIONS called:
46% 'varcivx_generator':, sets the names of vaiables to read in the netcdf file
47% 'nc2struct': reads a netcdf file
48
49function [Field,VelTypeOut,errormsg]=read_civdata(filename,FieldNames,VelType,CivStage)
50
51%% default input
52if ~exist('VelType','var')
53    VelType='';
54end
55if isequal(VelType,'*')
56    VelType='';
57end
58if isempty(VelType)
59    VelType='';
60end
61if ~exist('FieldNames','var')
62    FieldNames=[]; %default
63end
64errormsg='';
65
66%% reading data
67[varlist,role,units,VelTypeOut]=varcivx_generator(FieldNames,VelType,CivStage);
68if isempty(varlist)
69    erromsg=['error in read_civdata: unknow velocity type ' VelType];
70    return
71else
72    [Field,vardetect]=nc2struct(filename,varlist);%read the variables in the netcdf file
73end
74if isfield(Field,'Txt')
75    errormsg=Field.Txt;
76    return
77end
78if vardetect(1)==0
79     errormsg=[ 'requested field not available in ' filename '/' VelType ': need to run patch'];
80     return
81end
82switch VelTypeOut
83    case{'civ1','filter1'}
84        if isfield(Field,'Patch1_SubDomain')
85            Field.SubDomain=Field.Patch1_SubDomain;
86            Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}];
87        end     
88        Field.Dt=Field.Civ1_Dt;
89        Field.Time=Field.Civ1_Time;
90    case{'civ2','filter2'}
91        if isfield(Field,'Patch2_SubDomain')
92            Field.SubDomain=Field.Patch2_SubDomain;
93            Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'SubDomain'}];
94        end
95        Field.Dt=Field.Civ2_Dt;
96        Field.Time=Field.Civ2_Time;
97end
98Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'Dt','Time'}];
99var_ind=find(vardetect);
100for ivar=1:numel(var_ind)
101    Field.VarAttribute{ivar}.Role=role{var_ind(ivar)};
102    Field.VarAttribute{ivar}.Unit=units{var_ind(ivar)};
103    Field.VarAttribute{ivar}.Mesh=0.1;%typical mesh for histograms O.1 pixel
104end
105Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'NbCoord','NbDim','TimeUnit','CoordUnit'}];
106% %% update list of global attributes
107Field.NbCoord=2;
108Field.NbDim=2;
109Field.TimeUnit='s';
110Field.CoordUnit='pixel';
111
112%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
113% [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
114%INPUT:
115% FieldNames =cell of field names to get, which can contain the strings:
116%             'ima_cor': image correlation, vec_c or vec2_C
117%             'vort','div','strain': requires velocity derivatives DUDX...
118%             'error': error estimate (vec_E or vec2_E)
119%             
120% vel_type: character string indicating the types of velocity fields to read ('civ1','civ2'...)
121%            if vel_type=[] or'*', a  priority choice is done, civ2 considered better than civ1 )
122
123function [var,role,units,vel_type_out,errormsg]=varcivx_generator(FieldNames,vel_type,CivStage)
124
125%% default input values
126if ~exist('vel_type','var'),vel_type='';end;
127if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed
128if ~exist('FieldNames','var'),FieldNames={'ima_cor'};end;%default scalar
129if ischar(FieldNames), FieldNames={FieldNames}; end;
130errormsg='';
131
132%% select the priority order for automatic vel_type selection
133testder=0;
134testpatch=0;
135for ilist=1:length(FieldNames)
136    if ~isempty(FieldNames{ilist})
137        switch FieldNames{ilist}
138            case{'u','v'}
139                testpatch=1;
140            case {'vort','div','strain'}
141                testder=1;
142        end
143    end
144end
145if strcmp(vel_type,'civ2') && testder
146    vel_type='filter2';
147elseif strcmp(vel_type,'civ1') && testder
148    vel_type='filter1';
149end
150if isempty(vel_type)||strcmp(vel_type,'*')
151    switch CivStage
152        case {6} %filter2 available
153            vel_type='filter2';
154        case {4,5}% civ2 available but not filter2
155            if testder% derivatives needed
156                vel_type='filter1';
157            else
158                vel_type='civ2';
159            end
160        case 3
161            vel_type='filter1';
162        case {1,2}% civ1 available but not filter1
163            vel_type='civ1';
164    end
165end
166
167var={};
168switch vel_type
169    case 'civ1'
170        var={'X','Y','Z','U','V','W','C','F','FF';...
171            'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U','Civ1_V','Civ1_W','Civ1_C','Civ1_F','Civ1_FF'};
172        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
173        units={'pixel','pixel','pixel','pixel','pixel','pixel','','',''};
174    case 'filter1'
175        var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbSites';...
176            'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U_smooth','Civ1_V_smooth','Civ1_W','Civ1_C','Civ1_F','Civ1_FF',...
177            'Civ1_Coord_tps','Civ1_U_tps','Civ1_V_tps','Civ1_W_tps','Civ1_SubRange','Civ1_NbSites'};
178        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',...
179            'vector_y_tps','vector_z_tps','ancillary','ancillary'};
180        units={'pixel','pixel','pixel','pixel','pixel','pixel','','','','pixel','pixel','pixel','pixel','pixel',''};
181    case 'civ2'
182        var={'X','Y','Z','U','V','W','C','F','FF';...
183            'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U','Civ2_V','Civ2_W','Civ2_C','Civ2_F','Civ2_FF'};
184        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
185        units={'pixel','pixel','pixel','pixel','pixel','pixel','','',''};
186    case 'filter2'
187        var={'X','Y','Z','U','V','W','C','F','FF','Coord_tps','U_tps','V_tps','W_tps','SubRange','NbSites';...
188            'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U_smooth','Civ2_V_smooth','Civ2_W','Civ2_C','Civ2_F','Civ2_FF',...
189            'Civ2_Coord_tps','Civ2_U_tps','Civ2_V_tps','','Civ2_SubRange','Civ2_NbSites'};
190        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','coord_tps','vector_x_tps',...
191            'vector_y_tps','vector_z_tps','ancillary','ancillary'};
192        units={'pixel','pixel','pixel','pixel','pixel','pixel','','','','pixel','pixel','pixel','pixel','pixel',''};
193end
194vel_type_out=vel_type;
195
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