source: trunk/src/read_civxdata.m @ 456

Last change on this file since 456 was 420, checked in by sommeria, 12 years ago

bugs corrected for series: error display in case of input error
;

File size: 11.3 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,errormsg]=read_civxdata(filename,FieldNames,VelType)
50errormsg='';
51Field=[];
52VelTypeOut=[];
53DataTest=nc2struct(filename,'ListGlobalAttribute','Conventions','CivStage');
54if isfield(DataTest,'Txt')
55    errormsg=DataTest.Txt;
56    return
57elseif isequal(DataTest.Conventions,'uvmat/civdata')%test for new civ format
58     [Field,VelTypeOut,errormsg]=read_civdata(filename,FieldNames,VelType,DataTest.CivStage);
59%      if ~isempty(errormsg)
60%          msgbox_uvmat('ERROR',errormsg)
61%      end
62     return
63end
64   
65%% default input
66if ~exist('VelType','var')
67    VelType=[];
68end
69if isequal(VelType,'*')
70    VelType=[];
71end
72if ~exist('FieldNames','var')
73    FieldNames=[]; %default
74end
75
76%% reading data
77VelTypeOut=VelType;%default
78[var,role,units,vel_type_out_cell]=varcivx_generator(FieldNames,VelType);%determine the names of constants and variables to read
79[Field,vardetect,ichoice]=nc2struct(filename,var);%read the variables in the netcdf file
80if isfield(Field,'Txt')
81    errormsg=Field.Txt;
82    return
83end
84if vardetect(1)==0
85     errormsg=[ 'requested field not available in ' filename '/' VelType];
86     return
87end
88var_ind=find(vardetect);
89for ivar=1:length(var_ind)
90    Field.VarAttribute{ivar}.Role=role{var_ind(ivar)};
91    Field.VarAttribute{ivar}.Mesh=0.1;%typical mesh for histograms O.1 pixel
92end
93VelTypeOut=VelType;
94if ~isempty(ichoice)
95    VelTypeOut=vel_type_out_cell{ichoice};
96end
97
98%% adjust for Djui:
99if isfield(Field,'DjUi')
100    Field.ListVarName{end-3}='DjUi';
101    Field.VarDimName{end-3}=[Field.VarDimName{end-3} {'nb_coord'} {'nb-coord'}];
102    Field.ListVarName(end-2:end)=[];
103    Field.VarDimName(end-2:end)=[];
104    Field.VarAttribute(end-2:end)=[];
105end
106
107%% renaming for standard conventions
108Field.NbCoord=Field.nb_coord;
109Field.NbDim=Field.nb_dim;
110
111%% CivStage
112if isfield(Field,'patch2')&& isequal(Field.patch2,1)
113    Field.CivStage=6;
114elseif isfield(Field,'fix2')&& isequal(Field.fix2,1)
115    Field.CivStage=5;
116elseif isfield(Field,'civ2')&& isequal(Field.civ2,1)
117    Field.CivStage=4;
118elseif isfield(Field,'patch')&& isequal(Field.patch,1)
119    Field.CivStage=3;
120elseif isfield(Field,'fix')&& isequal(Field.fix,1)
121    Field.CivStage=2;
122else
123    Field.CivStage=1;
124end
125
126%determine the appropriate constant for time and dt for the PIV pair
127test_civ1=isequal(VelTypeOut,'civ1')||isequal(VelTypeOut,'interp1')||isequal(VelTypeOut,'filter1');
128test_civ2=isequal(VelTypeOut,'civ2')||isequal(VelTypeOut,'interp2')||isequal(VelTypeOut,'filter2');
129Field.Time=0; %default
130Field.TimeUnit='s';
131if test_civ1
132    if isfield(Field,'absolut_time_T0')
133        Field.Time=double(Field.absolut_time_T0);
134        Field.Dt=double(Field.dt);
135    else
136       errormsg='the input file is not civx';
137       Field.CivStage=0;
138       Field.Dt=0;
139    end
140elseif test_civ2
141    Field.Time=double(Field.absolut_time_T0_2);
142    Field.Dt=double(Field.dt2);
143else
144    errormsg='the input file is not civx';
145    Field.CivStage=0;
146    Field.Dt=0;
147end
148
149
150
151%% rescale fields to pixel coordinates
152if isfield(Field,'pixcmx')
153    Field.pixcmx=double(Field.pixcmx);
154    Field.pixcmy=double(Field.pixcmy);
155    Field.U=Field.U*Field.pixcmx;
156    Field.V=Field.V*Field.pixcmy;
157    Field.X=Field.X*Field.pixcmx;
158    Field.Y=Field.Y*Field.pixcmy;
159end
160if ~isequal(Field.dt,0)
161    Field.U=Field.U*Field.dt;%translate in px displacement
162    Field.V=Field.V*Field.dt;
163    if isfield(Field,'DjUi')
164       Field.DjUi(:,1,1)=Field.dt*Field.DjUi(:,1,1);
165       Field.DjUi(:,2,2)=Field.dt*Field.DjUi(:,2,2);
166       Field.DjUi(:,1,2)=(Field.pixcmy/Field.pixcmx)*Field.dt*Field.DjUi(:,1,2);
167       Field.DjUi(:,2,1)=(Field.pixcmx/Field.pixcmy)*Field.dt*Field.DjUi(:,2,1);
168    end
169end
170
171%% update list of global attributes
172List=Field.ListGlobalAttribute;
173ind_remove=[];
174for ilist=1:length(List)
175    switch(List{ilist})
176        case {'patch2','fix2','civ2','patch','fix','dt','dt2','absolut_time_T0','absolut_time_T0_2','nb_coord','nb_dim','pixcmx','pixcmy'}
177            ind_remove=[ind_remove ilist];
178            Field=rmfield(Field,List{ilist});
179    end
180end
181List(ind_remove)=[];
182Field.ListGlobalAttribute=[{'NbCoord'},{'NbDim'} List {'Time','Dt','TimeUnit','CivStage','CoordUnit'}];
183Field.CoordUnit='pixel';
184
185
186%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
187% [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
188%INPUT:
189% FieldNames =cell of field names to get, which can contain the strings:
190%             'ima_cor': image correlation, vec_c or vec2_C
191%             'vort','div','strain': requires velocity derivatives DUDX...
192%             'error': error estimate (vec_E or vec2_E)
193%             
194% vel_type: character string indicating the types of velocity fields to read ('civ1','civ2'...)
195%            if vel_type=[] or'*', a  priority choice, given by vel_type_out{1,2}, is done depending
196%            if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1)
197
198function [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
199
200%% default input values
201if ~exist('vel_type','var'),vel_type=[];end;
202if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed
203if ~exist('FieldNames','var'),FieldNames={'ima_cor'};end;%default scalar
204if ischar(FieldNames), FieldNames={FieldNames}; end;
205
206%% select the priority order for automatic vel_type selection
207testder=0;
208for ilist=1:length(FieldNames)
209    if ~isempty(FieldNames{ilist})
210    switch FieldNames{ilist}
211        case {'vort','div','strain'}
212            testder=1;
213    end
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%% determine names of netcdf variables to read
243var={'X','Y','Z','U','V','W','C','F','FF'};
244role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
245units={'pixel','pixel','pixel','pixel','pixel','pixel',[],[],[]};
246if testder
247    var=[var {'DjUi(:,1,1)','DjUi(:,1,2)','DjUi(:,2,1)','DjUi(:,2,2)'}];
248    role=[role {'tensor','tensor','tensor','tensor'}];
249    units=[units {'pixel','pixel','pixel','pixel'}];
250end
251for ilist=1:length(vel_type_out)
252    var=[var;varname1(vel_type_out{ilist},FieldNames)];
253end
254
255%------------------------------------------------------------------------ 
256%--- determine  var names to read
257function varin=varname1(vel_type,FieldNames)
258%------------------------------------------------------------------------
259testder=0;
260C1='';
261C2='';
262for ilist=1:length(FieldNames)
263    if ~isempty(FieldNames{ilist})
264    switch FieldNames{ilist}
265        case 'ima_cor' %image correlation corresponding to a vel vector
266            C1='vec_C';
267            C2='vec2_C';
268        case 'error'
269            C1='vec_E';
270            C2='vec2_E';
271        case {'vort','div','strain'}
272            testder=1;
273    end
274    end
275end     
276switch vel_type
277    case 'civ1'
278        varin={'vec_X','vec_Y','vec_Z','vec_U','vec_V','vec_W',C1,'vec_F','vec_FixFlag'};
279    case 'interp1'
280        varin={'vec_patch_X','vec_patch_Y','','vec_patch0_U','vec_patch0_V','','','',''};
281    case 'filter1'
282        varin={'vec_patch_X','vec_patch_Y','','vec_patch_U','vec_patch_V','','','',''};
283    case 'civ2'
284        varin={'vec2_X','vec2_Y','vec2_Z','vec2_U','vec2_V','vec2_W',C2,'vec2_F','vec2_FixFlag'};
285    case 'interp2'
286        varin={'vec2_patch_X','vec2_patch_Y','vec2_patch_Z','vec2_patch0_U','vec2_patch0_V','vec2_patch0_W','','',''};
287    case 'filter2'
288        varin={'vec2_patch_X','vec2_patch_Y','vec2_patch_Z','vec2_patch_U','vec2_patch_V','vec2_patch0_W','','',''};
289end
290if testder
291     switch vel_type
292        case 'filter1'
293            varin=[varin {'vec_patch_DUDX','vec_patch_DVDX','vec_patch_DUDY','vec_patch_DVDY'}];
294        case 'filter2'
295            varin=[varin {'vec2_patch_DUDX','vec2_patch_DVDX','vec2_patch_DUDY','vec2_patch_DVDY'}];
296    end   
297end
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