source: trunk/src/read_civdata.m @ 316

Last change on this file since 316 was 316, checked in by sommeria, 9 years ago

a few more bugs corrected, now the new civ_matlab works for civ1,fix1, patch1

File size: 10.1 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,XI,YI)
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,vel_type_out_cell]=varcivx_generator(FieldNames,VelType);
68[Field,vardetect,ichoice]=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];
75     return
76end
77var_ind=find(vardetect);
78for ivar=1:min(numel(var_ind),numel(Field.VarAttribute))
79    Field.VarAttribute{ivar}.Role=role{var_ind(ivar)};
80    Field.VarAttribute{ivar}.Unit=units{var_ind(ivar)};
81    Field.VarAttribute{ivar}.Mesh=0.1;%typical mesh for histograms O.1 pixel
82end
83if ~isempty(ichoice)
84    VelTypeOut=vel_type_out_cell{ichoice};
85end
86
87
88%% renaming for standard conventions
89%Field.NbCoord=Field.nb_coord;
90%Field.NbDim=2;%Field.nb_dim;
91
92%% CivStage
93% if isfield(Field,'patch2')&& isequal(Field.patch2,1)
94%     Field.CivStage=6;
95% elseif isfield(Field,'fix2')&& isequal(Field.fix2,1)
96%     Field.CivStage=5;
97% elseif isfield(Field,'civ2')&& isequal(Field.civ2,1)
98%     Field.CivStage=4;
99% elseif isfield(Field,'patch')&& isequal(Field.patch,1)
100%     Field.CivStage=3;
101% elseif isfield(Field,'fix')&& isequal(Field.fix,1)
102%     Field.CivStage=2;
103% else
104%     Field.CivStage=1;
105% end
106Field.ListGlobalAttribute=[Field.ListGlobalAttribute {'NbCoord','NbDim','TimeUnit','CoordUnit'}];
107% %determine the appropriate constant for time and dt for the PIV pair
108% test_civ1=isequal(VelTypeOut,'civ1')||isequal(VelTypeOut,'interp1')||isequal(VelTypeOut,'filter1');
109% test_civ2=isequal(VelTypeOut,'civ2')||isequal(VelTypeOut,'interp2')||isequal(VelTypeOut,'filter2');
110% Field.Time=0; %default
111% Field.TimeUnit='s';
112% if test_civ1
113%     if isfield(Field,'absolut_time_T0')
114%         Field.Time=double(Field.absolut_time_T0);
115%         Field.dt=double(Field.dt);
116%     else
117%        Field.Txt='the input file is not civx';
118%        Field.CivStage=0;
119%        Field.dt=0;
120%     end
121% elseif test_civ2
122%     Field.Time=double(Field.absolut_time_T0_2);
123%     Field.dt=double(Field.dt2);
124% else
125%     Field.Txt='the input file is not civx';
126%     Field.CivStage=0;
127%     Field.dt=0;
128% end
129%
130%
131%
132% %% update list of global attributes
133% List=Field.ListGlobalAttribute;
134% ind_remove=[];
135% for ilist=1:length(List)
136%     switch(List{ilist})
137%         case {'patch2','fix2','civ2','patch','fix','dt2','absolut_time_T0','absolut_time_T0_2','nb_coord','nb_dim','pixcmx','pixcmy'}
138%             ind_remove=[ind_remove ilist];
139%             Field=rmfield(Field,List{ilist});
140%     end
141% end
142% List(ind_remove)=[];
143% Field.ListGlobalAttribute=[{'NbCoord'},{'NbDim'} List {'Time','TimeUnit','CivStage','CoordUnit'}];
144Field.NbCoord=2;
145Field.NbDim=2;
146Field.TimeUnit='s';
147Field.CoordUnit='pixel';
148
149
150
151%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
152% TAKEN FROM read_civxdata NOT USED
153% [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
154%INPUT:
155% FieldNames =cell of field names to get, which can contain the strings:
156%             'ima_cor': image correlation, vec_c or vec2_C
157%             'vort','div','strain': requires velocity derivatives DUDX...
158%             'error': error estimate (vec_E or vec2_E)
159%             
160% vel_type: character string indicating the types of velocity fields to read ('civ1','civ2'...)
161%            if vel_type=[] or'*', a  priority choice, given by vel_type_out{1,2}, is done depending
162%            if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1)
163
164function [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
165
166%% default input values
167if ~exist('vel_type','var'),vel_type='';end;
168if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed
169if ~exist('FieldNames','var'),FieldNames={'ima_cor'};end;%default scalar
170if ischar(FieldNames), FieldNames={FieldNames}; end;
171
172%% select the priority order for automatic vel_type selection
173testder=0;
174testpatch=0;
175for ilist=1:length(FieldNames)
176    if ~isempty(FieldNames{ilist})
177    switch FieldNames{ilist}
178        case{'u','v'}
179            testpatch=1;
180        case {'vort','div','strain'}
181            testder=1;
182    end
183    end
184end   
185switch vel_type
186    case 'civ1'
187        var={'X','Y','Z','U','V','W','C','F','FF';...
188              'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U','Civ1_V','Civ1_W','Civ1_C','Civ1_F','Civ1_FF'};
189        role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
190        units={'pixel','pixel','pixel','pixel','pixel','pixel',[],[],[]};
191    case 'interp1'
192         var={'X','Y','Z','U','V','W','FF';...
193               'Civ1_X','Civ1_Y','','Civ1_U_Diff','Civ1_V_Diff','','Civ1_FF'};
194         role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','errorflag'}; 
195         units={'pixel','pixel','pixel','pixel','pixel','pixel',[]};
196    case 'filter1'
197        var={'X_tps','Y_tps','Z_tps','U_tps','V_tps','W_tps','X_SubRange','Y_SubRange','NbSites';...
198            'Civ1_X_tps','Civ1_Y_tps','','Civ1_U_tps','Civ1_V_tps','','Civ1_X_SubRange','Civ1_Y_SubRange','Civ1_NbSites'};
199         role={'','','','','','','','',''}; 
200         units={'pixel','pixel','pixel','pixel','pixel','pixel','pixel','pixel',''};
201    otherwise % if VelType=[]
202        if testpatch
203           var={'X_tps','Y_tps','Z_tps','U_tps','V_tps','W_tps','X_SubRange','Y_SubRange','NbSites';...
204               'Civ2_X_tps','Civ2_Y_tps','','Civ2_U_tps','Civ2_V_tps','','Civ2_X_SubRange','Civ2_Y_SubRange','Civ2_NbSites';...
205               'Civ1_X_tps','Civ1_Y_tps','','Civ1_U_tps','Civ1_V_tps','','Civ1_X_SubRange','Civ1_Y_SubRange','Civ1_NbSites'};
206            role={'','','','','','','',''}; 
207            units={'pixel','pixel','pixel','pixel','pixel','pixel','pixel','pixel'};
208        else
209             var={'X','Y','Z','U','V','W','C','F','FF';...
210              'Civ2_X','Civ2_Y','Civ2_Z','Civ2_U','Civ2_V','Civ2_W','Civ2_C','Civ2_F','Civ2_FF';...
211              'Civ1_X','Civ1_Y','Civ1_Z','Civ1_U','Civ1_V','Civ1_W','Civ1_C','Civ1_F','Civ1_FF'};
212            role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
213            units={'pixel','pixel','pixel','pixel','pixel','pixel',[],[],[]};
214        end   
215end
216if isempty(vel_type) || isequal(vel_type,'*') %undefined velocity type (civ1,civ2...)
217    if testder
218         vel_type_out{1}='filter2'; %priority to filter2 for scalar reading, filter1 as second
219        vel_type_out{2}='filter1';
220    else
221        vel_type_out{1}='civ2'; %priority to civ2 for vector reading, civ1 as second priority     
222        vel_type_out{2}='civ1';
223    end
224elseif isequal(vel_type,'filter')
225        vel_type_out{1}='filter2'; %priority to filter2 for scalar reading, filter1 as second
226        vel_type_out{2}='filter1';
227        if ~testder
228            vel_type_out{3}='civ1';%civ1 as third priority if derivatives are not needed
229        end
230elseif testder
231    test_civ1=isequal(vel_type,'civ1')||isequal(vel_type,'interp1')||isequal(vel_type,'filter1');
232    if test_civ1
233        vel_type_out{1}='filter1'; %switch to filter for reading spatial derivatives
234    else
235        vel_type_out{1}='filter2';
236    end
237else   
238    vel_type_out{1}=vel_type;%imposed velocity field
239end
240vel_type_out=vel_type_out';
241
242
243
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