source: trunk/src/read_civdata.m @ 382

Last change on this file since 382 was 382, checked in by sommeria, 12 years ago

several bugs corrected
function filter_tps introduced (spline thin shell)

File size: 9.0 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)
50errormsg='';
51VelTypeOut=VelType;%default
52%% default input
53if ~exist('VelType','var')
54    VelType='';
55end
56if isequal(VelType,'*')
57    VelType='';
58end
59if isempty(VelType)
60    VelType='';
61end
62if ~exist('FieldNames','var')
63    FieldNames=[]; %default
64end
65
66%% reading data
67[varlist,role,units,VelTypeOut]=varcivx_generator(FieldNames,VelType,CivStage);
68[Field,vardetect]=nc2struct(filename,varlist);%read the variables in the netcdf file
69if isfield(Field,'Txt')
70    errormsg=Field.Txt;
71    return
72end
73if vardetect(1)==0
74     errormsg=[ 'requested field not available in ' filename '/' VelType ': need to run patch'];
75     return
76end
77switch VelTypeOut
78    case{'civ1','civ-filter1','filter1'}
79        Field.Dt=Field.Civ1_Dt;
80    case{'civ2','civ-filter2','filter2'}
81        Field.Dt=Field.Civ2_Dt;
82end
83Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'Dt'}];
84var_ind=find(vardetect);
85for ivar=1:min(numel(var_ind),numel(Field.VarAttribute))
86    Field.VarAttribute{ivar}.Role=role{var_ind(ivar)};
87    Field.VarAttribute{ivar}.Unit=units{var_ind(ivar)};
88    Field.VarAttribute{ivar}.Mesh=0.1;%typical mesh for histograms O.1 pixel
89end
90
91Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'NbCoord','NbDim','TimeUnit','CoordUnit'}];
92% %% update list of global attributes
93Field.NbCoord=2;
94Field.NbDim=2;
95Field.TimeUnit='s';
96Field.CoordUnit='pixel';
97
98
99
100%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
101% [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
102%INPUT:
103% FieldNames =cell of field names to get, which can contain the strings:
104%             'ima_cor': image correlation, vec_c or vec2_C
105%             'vort','div','strain': requires velocity derivatives DUDX...
106%             'error': error estimate (vec_E or vec2_E)
107%             
108% vel_type: character string indicating the types of velocity fields to read ('civ1','civ2'...)
109%            if vel_type=[] or'*', a  priority choice is done, civ2 considered better than civ1 )
110
111function [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type,CivStage)
112
113%% default input values
114if ~exist('vel_type','var'),vel_type='';end;
115if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed
116if ~exist('FieldNames','var'),FieldNames={'ima_cor'};end;%default scalar
117if ischar(FieldNames), FieldNames={FieldNames}; end;
118
119%% select the priority order for automatic vel_type selection
120testder=0;
121testpatch=0;
122for ilist=1:length(FieldNames)
123    if ~isempty(FieldNames{ilist})
124    switch FieldNames{ilist}
125        case{'u','v'}
126            testpatch=1;
127        case {'vort','div','strain'}
128            testder=1;
129           
130    end
131    end
132end   
133
134if isempty(vel_type)
135    switch CivStage
136        case {6} %filter2 available
137            vel_type='civ2';
138        case {4,5}% civ2 available but not filter2
139            if testder% derivatives needed
140                vel_type='civ1';
141            else
142                vel_type='civ2';
143            end
144        case {1,2,3}% civ1 available but not civ2
145            vel_type='civ1';
146    end
147end
148if strcmp(vel_type,'civ2') && testder
149    vel_type='filter2';
150elseif strcmp(vel_type,'civ1') && testder
151    vel_type='filter1';
152end
153
154switch vel_type
155    case {'civ1','filter1'}
156        var={'X','Y','Z','U','V','W','C','F','FF','X_tps','Y_tps','Z_tps','U_tps','V_tps','W_tps','X_SubRange','Y_SubRange','NbSites','Indices_tps';...
157            'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U','Civ1_V','Civ1_W','Civ1_C','Civ1_F','Civ1_FF',...
158            'Civ1_X_tps','Civ1_Y_tps','','Civ1_U_tps','Civ1_V_tps','','Civ1_X_SubRange','Civ1_Y_SubRange','Civ1_NbSites','Civ1_Indices_tps'};
159        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','','','','','','','','','',''};
160        units={'pixel','pixel','pixel','pixel','pixel','pixel','','','','pixel','pixel','pixel','pixel','pixel','pixel','pixel','pixel','',''};
161    case 'civ-filter1'
162        var={'X','Y','Z','U','V','W','FF';...
163            'Civ1_X','Civ1_Y','','Civ1_U_Diff','Civ1_V_Diff','','Civ1_FF'};
164        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','errorflag'};
165        units={'pixel','pixel','pixel','pixel','pixel','pixel',[]};
166%     case 'filter1'
167%         var={'X_tps','Y_tps','Z_tps','U_tps','V_tps','W_tps','X_SubRange','Y_SubRange','NbSites','Indices_tps';...
168%             'Civ1_X_tps','Civ1_Y_tps','','Civ1_U_tps','Civ1_V_tps','','Civ1_X_SubRange','Civ1_Y_SubRange','Civ1_NbSites','Civ1_Indices_tps'};
169%         role={'','','','','','','','','',''};
170%         units={'pixel','pixel','pixel','pixel','pixel','pixel','pixel','pixel','',''};
171    case {'civ2','filter2'}
172        var={'X','Y','Z','U','V','W','C','F','FF','X_tps','Y_tps','Z_tps','U_tps','V_tps','W_tps','X_SubRange','Y_SubRange','NbSites','Indices_tps';...
173            'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U','Civ2_V','Civ2_W','Civ2_C','Civ2_F','Civ2_FF',...
174            'Civ2_X_tps','Civ2_Y_tps','','Civ2_U_tps','Civ2_V_tps','','Civ2_X_SubRange','Civ2_Y_SubRange','Civ2_NbSites','Civ2_Indices_tps'};
175        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag','','','','','','','','','',''};
176        units={'pixel','pixel','pixel','pixel','pixel','pixel','','','','pixel','pixel','pixel','pixel','pixel','pixel','pixel','pixel','',''};
177%         var={'X','Y','Z','U','V','W','C','F','FF';...
178%             'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U','Civ2_V','Civ2_W','Civ2_C','Civ2_F','Civ2_FF'};
179%         role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
180%         units={'pixel','pixel','pixel','pixel','pixel','pixel',[],[],[]};
181    case 'civ-filter2'
182        var={'X','Y','Z','U','V','W','FF';...
183            'Civ2_X','Civ2_Y','','Civ2_U_Diff','Civ2_V_Diff','','Civ2_FF'};
184        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','errorflag'};
185        units={'pixel','pixel','pixel','pixel','pixel','pixel',[]};
186%     case 'filter2'
187%         var={'X_tps','Y_tps','Z_tps','U_tps','V_tps','W_tps','X_SubRange','Y_SubRange','NbSites','Indices_tps';...
188%             'Civ2_X_tps','Civ2_Y_tps','','Civ2_U_tps','Civ2_V_tps','','Civ2_X_SubRange','Civ2_Y_SubRange','Civ2_NbSites','Civ2_Indices_tps'};
189%         role={'','','','','','','','','',''};
190%         units={'pixel','pixel','pixel','pixel','pixel','pixel','pixel','pixel','',''};
191end
192vel_type_out=vel_type;
193
194
195
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