source: trunk/src/read_civxdata.m @ 179

Last change on this file since 179 was 179, checked in by sommeria, 14 years ago

various bug repairs, in particular for 3D fields

File size: 10.4 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
51if ~exist('VelType','var')
52    VelType=[];
53end
54if isequal(VelType,'*')
55    VelType=[];
56end
57if ~exist('FieldNames','var')
58    FieldNames=[]; %default
59end
60VelTypeOut=VelType;%default
61[var,role,units,vel_type_out_cell]=varcivx_generator(FieldNames,VelType);%determine the names of constants and variables to read
62[Field,vardetect,ichoice]=nc2struct(filename,var);
63if isfield(Field,'Txt')
64    return % error in file reading
65end
66if vardetect(1)==0
67     Field.Txt=[ 'requested field not available in ' filename '/' VelType];
68     return
69end
70var_ind=find(vardetect);
71for ivar=1:length(var_ind)
72    Field.VarAttribute{ivar}.Role=role{var_ind(ivar)};
73%     Field.VarAttribute{ivar}.units=units{var_ind(ivar)};% not necessary: set with calc_field
74end
75VelTypeOut=VelType;
76if ~isempty(ichoice)
77    VelTypeOut=vel_type_out_cell{ichoice};
78end
79
80%adjust for Djui:
81if isfield(Field,'DjUi')
82    Field.ListVarName(end-2:end)=[];
83    Field.ListVarName{end}='DjUi';
84    Field.VarDimName(end-2:end)=[];
85    Field.VarAttribute(end-2:end)=[];
86end
87
88%renaiming for standard conventions
89Field.NbCoord=Field.nb_coord;
90Field.NbDim=Field.nb_dim;
91
92%determine the appropriate constant for time and dt for the PIV pair
93test_civ1=isequal(VelTypeOut,'civ1')||isequal(VelTypeOut,'interp1')||isequal(VelTypeOut,'filter1');
94test_civ2=isequal(VelTypeOut,'civ2')||isequal(VelTypeOut,'interp2')||isequal(VelTypeOut,'filter2');
95if test_civ1
96    Field.Time=double(Field.absolut_time_T0);
97    Field.dt=double(Field.dt);
98elseif test_civ2
99    Field.Time=double(Field.absolut_time_T0_2);
100    Field.dt=double(Field.dt2);
101else
102    Field.Txt='the input file is not civx';
103    display(Field.Txt)
104end
105
106% CivStage
107if isfield(Field,'patch2')&& isequal(Field.patch2,1)
108    Field.CivStage=6;
109elseif isfield(Field,'fix2')&& isequal(Field.fix2,1)
110    Field.CivStage=5;
111elseif isfield(Field,'civ2')&& isequal(Field.civ2,1)
112    Field.CivStage=4;
113elseif isfield(Field,'patch')&& isequal(Field.patch,1)
114    Field.CivStage=3;
115elseif isfield(Field,'fix')&& isequal(Field.fix,1)
116    Field.CivStage=2;
117else
118    Field.CivStage=1;
119end
120
121%% rescale fields to pixel coordinates
122if isfield(Field,'pixcmx')
123    Field.pixcmx=double(Field.pixcmx);
124    Field.pixcmy=double(Field.pixcmy);
125    Field.U=Field.U*Field.pixcmx;
126    Field.V=Field.V*Field.pixcmy;
127    Field.X=Field.X*Field.pixcmx;
128    Field.Y=Field.Y*Field.pixcmy;
129end
130if ~isequal(Field.dt,0)
131    Field.U=Field.U*Field.dt;%translate in px displacement
132    Field.V=Field.V*Field.dt;
133    if isfield(Field,'DjUi')
134       Field.DjUi(:,1,1)=Field.dt*Field.DjUi(:,1,1);
135       Field.DjUi(:,2,2)=Field.dt*Field.DjUi(:,2,2);
136       Field.DjUi(:,1,2)=(Field.pixcmy/Field.pixcmx)*Field.dt*Field.DjUi(:,1,2);
137       Field.DjUi(:,2,1)=(Field.pixcmx/Field.pixcmy)*Field.dt*Field.DjUi(:,2,1);
138    end
139end
140
141%% update list of global attributes
142List=Field.ListGlobalAttribute;
143ind_remove=[];
144for ilist=1:length(List)
145    switch(List{ilist})
146        case {'patch2','fix2','civ2','patch','fix','dt2','absolut_time_T0','absolut_time_T0_2','nb_coord','nb_dim','pixcmx','pixcmy'}
147            ind_remove=[ind_remove ilist];
148            Field=rmfield(Field,List{ilist});
149    end
150end
151List(ind_remove)=[];
152Field.ListGlobalAttribute=[{'NbCoord'},{'NbDim'} List {'Time','CivStage','CoordUnit'}];
153Field.CoordUnit='pixel';
154
155
156%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
157% [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
158%INPUT:
159% FieldNames =cell of field names to get, which can contain the strings:
160%             'ima_cor': image correlation, vec_c or vec2_C
161%             'vort','div','strain': requires velocity derivatives DUDX...
162%             'error': error estimate (vec_E or vec2_E)
163%             
164% vel_type: character string indicating the types of velocity fields to read ('civ1','civ2'...)
165%            if vel_type=[] or'*', a  priority choice, given by vel_type_out{1,2}, is done depending
166%            if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1)
167
168function [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
169
170%default input values
171if ~exist('vel_type','var'),vel_type=[];end;
172if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed
173% if ~exist('display','var'),display=[];end;
174if ~exist('FieldNames','var'),FieldNames={'ima_cor'};end;%default scalar
175if ischar(FieldNames), FieldNames={FieldNames}; end;
176
177%select the priority order for automatic vel_type selection
178testder=0;
179for ilist=1:length(FieldNames)
180    if ~isempty(FieldNames{ilist})
181    switch FieldNames{ilist}
182        case {'vort','div','strain'}
183            testder=1;
184    end
185    end
186end     
187if isempty(vel_type) || isequal(vel_type,'*') %undefined velocity type (civ1,civ2...)
188    if testder
189         vel_type_out{1}='filter2'; %priority to filter2 for scalar reading, filter1 as second
190        vel_type_out{2}='filter1';
191    else
192        vel_type_out{1}='civ2'; %priority to civ2 for vector reading, civ1 as second priority     
193        vel_type_out{2}='civ1';
194    end
195elseif isequal(vel_type,'filter')
196        vel_type_out{1}='filter2'; %priority to filter2 for scalar reading, filter1 as second
197        vel_type_out{2}='filter1';
198        if ~testder
199            vel_type_out{3}='civ1';%civ1 as third priority if derivatives are not needed
200        end
201elseif testder
202    test_civ1=isequal(vel_type,'civ1')||isequal(vel_type,'interp1')||isequal(vel_type,'filter1');
203    if test_civ1
204        vel_type_out{1}='filter1'; %switch to filter for reading spatial derivatives
205    else
206        vel_type_out{1}='filter2';
207    end
208else   
209    vel_type_out{1}=vel_type;%imposed velocity field
210end
211vel_type_out=vel_type_out';
212
213%determine names of netcdf variables to read
214var={'X','Y','Z','U','V','W','C','F','FF'};
215role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
216units={'pixel','pixel','pixel','pixel','pixel','pixel',[],[],[]};
217if testder
218    var=[var {'DjUi(:,1,1)','DjUi(:,1,2)','DjUi(:,2,1)','DjUi(:,2,2)'}];
219    role=[role {'tensor','tensor','tensor','tensor'}];
220    units=[units {'pixel','pixel','pixel','pixel'}];
221end
222for ilist=1:length(vel_type_out)
223    var=[var;varname1(vel_type_out{ilist},FieldNames)];
224end
225
226 
227%-------------------------
228%determine  var names to read
229%--------------------------------------
230function varin=varname1(vel_type,FieldNames)
231
232testder=0;
233C1='';
234C2='';
235for ilist=1:length(FieldNames)
236    if ~isempty(FieldNames{ilist})
237    switch FieldNames{ilist}
238        case 'ima_cor' %image correlation corresponding to a vel vector
239            C1='vec_C';
240            C2='vec2_C';
241        case 'error'
242            C1='vec_E';
243            C2='vec2_E';
244        case {'vort','div','strain'}
245            testder=1;
246    end
247    end
248end     
249switch vel_type
250    case 'civ1'
251        varin={'vec_X','vec_Y','vec_Z','vec_U','vec_V','vec_W',C1,'vec_F','vec_FixFlag'};
252    case 'interp1'
253        varin={'vec_patch_X','vec_patch_Y','','vec_patch0_U','vec_patch0_V','','','',''};
254    case 'filter1'
255        varin={'vec_patch_X','vec_patch_Y','','vec_patch_U','vec_patch_V','','','',''};
256    case 'civ2'
257        varin={'vec2_X','vec2_Y','vec2_Z','vec2_U','vec2_V','vec2_W',C2,'vec2_F','vec2_FixFlag'};
258    case 'interp2'
259        varin={'vec2_patch_X','vec2_patch_Y','vec2_patch_Z','vec2_patch0_U','vec2_patch0_V','vec2_patch0_W','','',''};
260    case 'filter2'
261        varin={'vec2_patch_X','vec2_patch_Y','vec2_patch_Z','vec2_patch_U','vec2_patch_V','vec2_patch0_W','','',''};
262end
263if testder
264     switch vel_type
265        case 'filter1'
266            varin=[varin {'vec_patch_DUDX','vec_patch_DVDX','vec_patch_DUDY','vec_patch_DVDY'}];
267        case 'filter2'
268            varin=[varin {'vec2_patch_DUDX','vec2_patch_DVDX','vec2_patch_DUDY','vec2_patch_DVDY'}];
269    end   
270end
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