source: trunk/src/read_civxdata.m @ 221

Last change on this file since 221 was 221, checked in by sommeria, 14 years ago

various bug corrections.

File size: 10.7 KB
Line 
1%'read_civxdata': reads civx 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]=read_civxdata(filename,FieldNames,VelType)
50%% default input
51if ~exist('VelType','var')
52    VelType=[];
53end
54if isequal(VelType,'*')
55    VelType=[];
56end
57if ~exist('FieldNames','var')
58    FieldNames=[]; %default
59end
60
61%% reading data
62VelTypeOut=VelType;%default
63[var,role,units,vel_type_out_cell]=varcivx_generator(FieldNames,VelType);%determine the names of constants and variables to read
64[Field,vardetect,ichoice]=nc2struct(filename,var);%read the variables in the netcdf file
65if isfield(Field,'Txt')
66    return
67end
68if vardetect(1)==0
69     Field.Txt=[ 'requested field not available in ' filename '/' VelType];
70     return
71end
72var_ind=find(vardetect);
73for ivar=1:length(var_ind)
74    Field.VarAttribute{ivar}.Role=role{var_ind(ivar)};
75    Field.VarAttribute{ivar}.Mesh=0.1;%typical mesh for histograms O.1 pixel
76end
77VelTypeOut=VelType;
78if ~isempty(ichoice)
79    VelTypeOut=vel_type_out_cell{ichoice};
80end
81
82%% adjust for Djui:
83if isfield(Field,'DjUi')
84    Field.ListVarName(end-2:end)=[];
85    Field.ListVarName{end}='DjUi';
86    Field.VarDimName(end-2:end)=[];
87    Field.VarAttribute(end-2:end)=[];
88end
89
90%% renaming for standard conventions
91Field.NbCoord=Field.nb_coord;
92Field.NbDim=Field.nb_dim;
93
94%% CivStage
95if isfield(Field,'patch2')&& isequal(Field.patch2,1)
96    Field.CivStage=6;
97elseif isfield(Field,'fix2')&& isequal(Field.fix2,1)
98    Field.CivStage=5;
99elseif isfield(Field,'civ2')&& isequal(Field.civ2,1)
100    Field.CivStage=4;
101elseif isfield(Field,'patch')&& isequal(Field.patch,1)
102    Field.CivStage=3;
103elseif isfield(Field,'fix')&& isequal(Field.fix,1)
104    Field.CivStage=2;
105else
106    Field.CivStage=1;
107end
108
109%determine the appropriate constant for time and dt for the PIV pair
110test_civ1=isequal(VelTypeOut,'civ1')||isequal(VelTypeOut,'interp1')||isequal(VelTypeOut,'filter1');
111test_civ2=isequal(VelTypeOut,'civ2')||isequal(VelTypeOut,'interp2')||isequal(VelTypeOut,'filter2');
112Field.Time=0; %default
113Field.TimeUnit='s';
114if test_civ1
115    if isfield(Field,'absolut_time_T0')
116        Field.Time=double(Field.absolut_time_T0);
117        Field.dt=double(Field.dt);
118    else
119       Field.Txt='the input file is not civx';
120       Field.CivStage=0;
121       Field.dt=0;
122    end
123elseif test_civ2
124    Field.Time=double(Field.absolut_time_T0_2);
125    Field.dt=double(Field.dt2);
126else
127    Field.Txt='the input file is not civx';
128    Field.CivStage=0;
129    Field.dt=0;
130end
131
132
133
134%% rescale fields to pixel coordinates
135if isfield(Field,'pixcmx')
136    Field.pixcmx=double(Field.pixcmx);
137    Field.pixcmy=double(Field.pixcmy);
138    Field.U=Field.U*Field.pixcmx;
139    Field.V=Field.V*Field.pixcmy;
140    Field.X=Field.X*Field.pixcmx;
141    Field.Y=Field.Y*Field.pixcmy;
142end
143if ~isequal(Field.dt,0)
144    Field.U=Field.U*Field.dt;%translate in px displacement
145    Field.V=Field.V*Field.dt;
146    if isfield(Field,'DjUi')
147       Field.DjUi(:,1,1)=Field.dt*Field.DjUi(:,1,1);
148       Field.DjUi(:,2,2)=Field.dt*Field.DjUi(:,2,2);
149       Field.DjUi(:,1,2)=(Field.pixcmy/Field.pixcmx)*Field.dt*Field.DjUi(:,1,2);
150       Field.DjUi(:,2,1)=(Field.pixcmx/Field.pixcmy)*Field.dt*Field.DjUi(:,2,1);
151    end
152end
153
154%% update list of global attributes
155List=Field.ListGlobalAttribute;
156ind_remove=[];
157for ilist=1:length(List)
158    switch(List{ilist})
159        case {'patch2','fix2','civ2','patch','fix','dt2','absolut_time_T0','absolut_time_T0_2','nb_coord','nb_dim','pixcmx','pixcmy'}
160            ind_remove=[ind_remove ilist];
161            Field=rmfield(Field,List{ilist});
162    end
163end
164List(ind_remove)=[];
165Field.ListGlobalAttribute=[{'NbCoord'},{'NbDim'} List {'Time','TimeUnit','CivStage','CoordUnit'}];
166Field.CoordUnit='pixel';
167
168
169%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
170% [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
171%INPUT:
172% FieldNames =cell of field names to get, which can contain the strings:
173%             'ima_cor': image correlation, vec_c or vec2_C
174%             'vort','div','strain': requires velocity derivatives DUDX...
175%             'error': error estimate (vec_E or vec2_E)
176%             
177% vel_type: character string indicating the types of velocity fields to read ('civ1','civ2'...)
178%            if vel_type=[] or'*', a  priority choice, given by vel_type_out{1,2}, is done depending
179%            if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1)
180
181function [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
182
183%% default input values
184if ~exist('vel_type','var'),vel_type=[];end;
185if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed
186if ~exist('FieldNames','var'),FieldNames={'ima_cor'};end;%default scalar
187if ischar(FieldNames), FieldNames={FieldNames}; end;
188
189%% select the priority order for automatic vel_type selection
190testder=0;
191for ilist=1:length(FieldNames)
192    if ~isempty(FieldNames{ilist})
193    switch FieldNames{ilist}
194        case {'vort','div','strain'}
195            testder=1;
196    end
197    end
198end     
199if isempty(vel_type) || isequal(vel_type,'*') %undefined velocity type (civ1,civ2...)
200    if testder
201         vel_type_out{1}='filter2'; %priority to filter2 for scalar reading, filter1 as second
202        vel_type_out{2}='filter1';
203    else
204        vel_type_out{1}='civ2'; %priority to civ2 for vector reading, civ1 as second priority     
205        vel_type_out{2}='civ1';
206    end
207elseif isequal(vel_type,'filter')
208        vel_type_out{1}='filter2'; %priority to filter2 for scalar reading, filter1 as second
209        vel_type_out{2}='filter1';
210        if ~testder
211            vel_type_out{3}='civ1';%civ1 as third priority if derivatives are not needed
212        end
213elseif testder
214    test_civ1=isequal(vel_type,'civ1')||isequal(vel_type,'interp1')||isequal(vel_type,'filter1');
215    if test_civ1
216        vel_type_out{1}='filter1'; %switch to filter for reading spatial derivatives
217    else
218        vel_type_out{1}='filter2';
219    end
220else   
221    vel_type_out{1}=vel_type;%imposed velocity field
222end
223vel_type_out=vel_type_out';
224
225%% determine names of netcdf variables to read
226var={'X','Y','Z','U','V','W','C','F','FF'};
227role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
228units={'pixel','pixel','pixel','pixel','pixel','pixel',[],[],[]};
229if testder
230    var=[var {'DjUi(:,1,1)','DjUi(:,1,2)','DjUi(:,2,1)','DjUi(:,2,2)'}];
231    role=[role {'tensor','tensor','tensor','tensor'}];
232    units=[units {'pixel','pixel','pixel','pixel'}];
233end
234for ilist=1:length(vel_type_out)
235    var=[var;varname1(vel_type_out{ilist},FieldNames)];
236end
237
238%------------------------------------------------------------------------ 
239%--- determine  var names to read
240function varin=varname1(vel_type,FieldNames)
241%------------------------------------------------------------------------
242testder=0;
243C1='';
244C2='';
245for ilist=1:length(FieldNames)
246    if ~isempty(FieldNames{ilist})
247    switch FieldNames{ilist}
248        case 'ima_cor' %image correlation corresponding to a vel vector
249            C1='vec_C';
250            C2='vec2_C';
251        case 'error'
252            C1='vec_E';
253            C2='vec2_E';
254        case {'vort','div','strain'}
255            testder=1;
256    end
257    end
258end     
259switch vel_type
260    case 'civ1'
261        varin={'vec_X','vec_Y','vec_Z','vec_U','vec_V','vec_W',C1,'vec_F','vec_FixFlag'};
262    case 'interp1'
263        varin={'vec_patch_X','vec_patch_Y','','vec_patch0_U','vec_patch0_V','','','',''};
264    case 'filter1'
265        varin={'vec_patch_X','vec_patch_Y','','vec_patch_U','vec_patch_V','','','',''};
266    case 'civ2'
267        varin={'vec2_X','vec2_Y','vec2_Z','vec2_U','vec2_V','vec2_W',C2,'vec2_F','vec2_FixFlag'};
268    case 'interp2'
269        varin={'vec2_patch_X','vec2_patch_Y','vec2_patch_Z','vec2_patch0_U','vec2_patch0_V','vec2_patch0_W','','',''};
270    case 'filter2'
271        varin={'vec2_patch_X','vec2_patch_Y','vec2_patch_Z','vec2_patch_U','vec2_patch_V','vec2_patch0_W','','',''};
272end
273if testder
274     switch vel_type
275        case 'filter1'
276            varin=[varin {'vec_patch_DUDX','vec_patch_DVDX','vec_patch_DUDY','vec_patch_DVDY'}];
277        case 'filter2'
278            varin=[varin {'vec2_patch_DUDX','vec2_patch_DVDX','vec2_patch_DUDY','vec2_patch_DVDY'}];
279    end   
280end
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