source: trunk/src/read_civxdata.m @ 501

Last change on this file since 501 was 498, checked in by sommeria, 9 years ago

various bug corrections, compatibilty with older PIV data

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=['nc2struct:' 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),errormsg=['read_civdata:' errormsg];end
60     return
61end
62   
63%% default input
64if ~exist('VelType','var')
65    VelType=[];
66end
67if isequal(VelType,'*')
68    VelType=[];
69end
70if ~exist('FieldNames','var')
71    FieldNames=[]; %default
72end
73
74%% reading data
75VelTypeOut=VelType;%default
76[var,role,units,vel_type_out_cell]=varcivx_generator(FieldNames,VelType);%determine the names of constants and variables to read
77[Field,vardetect,ichoice]=nc2struct(filename,var);%read the variables in the netcdf file
78if isfield(Field,'Txt')
79    errormsg=['nc2struct:' Field.Txt];
80    return
81end
82if vardetect(1)==0
83     errormsg=[ 'requested field not available in ' filename '/' VelType];
84     return
85end
86var_ind=find(vardetect);
87for ivar=1:length(var_ind)
88    Field.VarAttribute{ivar}.Role=role{var_ind(ivar)};
89    Field.VarAttribute{ivar}.Mesh=0.1;%typical mesh for histograms O.1 pixel
90end
91VelTypeOut=VelType;
92if ~isempty(ichoice)
93    VelTypeOut=vel_type_out_cell{ichoice};
94end
95
96%% adjust for Djui:
97if isfield(Field,'DjUi')
98    Field.ListVarName{end-3}='DjUi';
99    Field.VarDimName{end-3}=[Field.VarDimName{end-3} {'nb_coord'} {'nb-coord'}];
100    Field.ListVarName(end-2:end)=[];
101    Field.VarDimName(end-2:end)=[];
102    Field.VarAttribute(end-2:end)=[];
103end
104
105%% renaming for standard conventions
106Field.NbCoord=Field.nb_coord;
107Field.NbDim=Field.nb_dim;
108
109%% CivStage
110if isfield(Field,'patch2')&& isequal(Field.patch2,1)
111    Field.CivStage=6;
112elseif isfield(Field,'fix2')&& isequal(Field.fix2,1)
113    Field.CivStage=5;
114elseif isfield(Field,'civ2')&& isequal(Field.civ2,1)
115    Field.CivStage=4;
116elseif isfield(Field,'patch')&& isequal(Field.patch,1)
117    Field.CivStage=3;
118elseif isfield(Field,'fix')&& isequal(Field.fix,1)
119    Field.CivStage=2;
120else
121    Field.CivStage=1;
122end
123
124%determine the appropriate constant for time and dt for the PIV pair
125test_civ1=isequal(VelTypeOut,'civ1')||isequal(VelTypeOut,'interp1')||isequal(VelTypeOut,'filter1');
126test_civ2=isequal(VelTypeOut,'civ2')||isequal(VelTypeOut,'interp2')||isequal(VelTypeOut,'filter2');
127Field.Time=0; %default
128Field.TimeUnit='s';
129if test_civ1
130    if isfield(Field,'absolut_time_T0')
131        Field.Time=double(Field.absolut_time_T0);
132        Field.Dt=double(Field.dt);
133    else
134       errormsg='the input file is not civx';
135       Field.CivStage=0;
136       Field.Dt=0;
137    end
138elseif test_civ2
139    Field.Time=double(Field.absolut_time_T0_2);
140    Field.Dt=double(Field.dt2);
141else
142    errormsg='the input file is not civx';
143    Field.CivStage=0;
144    Field.Dt=0;
145end
146
147
148
149%% rescale fields to pixel coordinates
150if isfield(Field,'pixcmx')
151    Field.pixcmx=double(Field.pixcmx);
152    Field.pixcmy=double(Field.pixcmy);
153    Field.U=Field.U*Field.pixcmx;
154    Field.V=Field.V*Field.pixcmy;
155    Field.X=Field.X*Field.pixcmx;
156    Field.Y=Field.Y*Field.pixcmy;
157end
158if ~isequal(Field.Dt,0)
159    Field.U=Field.U*Field.Dt;%translate in px displacement
160    Field.V=Field.V*Field.Dt;
161    if isfield(Field,'DjUi')
162       Field.DjUi(:,1,1)=Field.Dt*Field.DjUi(:,1,1);
163       Field.DjUi(:,2,2)=Field.Dt*Field.DjUi(:,2,2);
164       Field.DjUi(:,1,2)=(Field.pixcmy/Field.pixcmx)*Field.Dt*Field.DjUi(:,1,2);
165       Field.DjUi(:,2,1)=(Field.pixcmx/Field.pixcmy)*Field.Dt*Field.DjUi(:,2,1);
166    end
167end
168
169%% update list of global attributes
170List=Field.ListGlobalAttribute;
171ind_remove=[];
172for ilist=1:length(List)
173    switch(List{ilist})
174        case {'patch2','fix2','civ2','patch','fix','dt','dt2','absolut_time_T0','absolut_time_T0_2','nb_coord','nb_dim','pixcmx','pixcmy'}
175            ind_remove=[ind_remove ilist];
176            Field=rmfield(Field,List{ilist});
177    end
178end
179List(ind_remove)=[];
180Field.ListGlobalAttribute=[{'NbCoord'},{'NbDim'} List {'Time','Dt','TimeUnit','CivStage','CoordUnit'}];
181Field.CoordUnit='pixel';
182
183
184%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
185% [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
186%INPUT:
187% FieldNames =cell of field names to get, which can contain the strings:
188%             'ima_cor': image correlation, vec_c or vec2_C
189%             'vort','div','strain': requires velocity derivatives DUDX...
190%             'error': error estimate (vec_E or vec2_E)
191%             
192% vel_type: character string indicating the types of velocity fields to read ('civ1','civ2'...)
193%            if vel_type=[] or'*', a  priority choice, given by vel_type_out{1,2}, is done depending
194%            if vel_type='filter'; a structured field is sought (filter2 in priority, then filter1)
195
196function [var,role,units,vel_type_out]=varcivx_generator(FieldNames,vel_type)
197
198%% default input values
199if ~exist('vel_type','var'),vel_type=[];end;
200if iscell(vel_type),vel_type=vel_type{1}; end;%transform cell to string if needed
201if ~exist('FieldNames','var'),FieldNames={'ima_cor'};end;%default scalar
202if ischar(FieldNames), FieldNames={FieldNames}; end;
203
204%% select the priority order for automatic vel_type selection
205testder=0;
206for ilist=1:length(FieldNames)
207    if ~isempty(FieldNames{ilist})
208    switch FieldNames{ilist}
209        case {'vort','div','strain'}
210            testder=1;
211    end
212    end
213end     
214if isempty(vel_type) || isequal(vel_type,'*') %undefined velocity type (civ1,civ2...)
215    if testder
216         vel_type_out{1}='filter2'; %priority to filter2 for scalar reading, filter1 as second
217        vel_type_out{2}='filter1';
218    else
219        vel_type_out{1}='civ2'; %priority to civ2 for vector reading, civ1 as second priority     
220        vel_type_out{2}='civ1';
221    end
222elseif isequal(vel_type,'filter')
223        vel_type_out{1}='filter2'; %priority to filter2 for scalar reading, filter1 as second
224        vel_type_out{2}='filter1';
225        if ~testder
226            vel_type_out{3}='civ1';%civ1 as third priority if derivatives are not needed
227        end
228elseif testder
229    test_civ1=isequal(vel_type,'civ1')||isequal(vel_type,'interp1')||isequal(vel_type,'filter1');
230    if test_civ1
231        vel_type_out{1}='filter1'; %switch to filter for reading spatial derivatives
232    else
233        vel_type_out{1}='filter2';
234    end
235else   
236    vel_type_out{1}=vel_type;%imposed velocity field
237end
238vel_type_out=vel_type_out';
239
240%% determine names of netcdf variables to read
241var={'X','Y','Z','U','V','W','C','F','FF'};
242role={'coord_x','coord_y','coord_z','vector_x','vector_y','vector_z','ancillary','warnflag','errorflag'};
243units={'pixel','pixel','pixel','pixel','pixel','pixel',[],[],[]};
244if testder
245    var=[var {'DjUi(:,1,1)','DjUi(:,1,2)','DjUi(:,2,1)','DjUi(:,2,2)'}];
246    role=[role {'tensor','tensor','tensor','tensor'}];
247    units=[units {'pixel','pixel','pixel','pixel'}];
248end
249for ilist=1:length(vel_type_out)
250    var=[var;varname1(vel_type_out{ilist},FieldNames)];
251end
252
253%------------------------------------------------------------------------ 
254%--- determine  var names to read
255function varin=varname1(vel_type,FieldNames)
256%------------------------------------------------------------------------
257testder=0;
258C1='';
259C2='';
260for ilist=1:length(FieldNames)
261    if ~isempty(FieldNames{ilist})
262    switch FieldNames{ilist}
263        case 'ima_cor' %image correlation corresponding to a vel vector
264            C1='vec_C';
265            C2='vec2_C';
266        case 'error'
267            C1='vec_E';
268            C2='vec2_E';
269        case {'vort','div','strain'}
270            testder=1;
271    end
272    end
273end     
274switch vel_type
275    case 'civ1'
276        varin={'vec_X','vec_Y','vec_Z','vec_U','vec_V','vec_W',C1,'vec_F','vec_FixFlag'};
277    case 'interp1'
278        varin={'vec_patch_X','vec_patch_Y','','vec_patch0_U','vec_patch0_V','','','',''};
279    case 'filter1'
280        varin={'vec_patch_X','vec_patch_Y','','vec_patch_U','vec_patch_V','','','',''};
281    case 'civ2'
282        varin={'vec2_X','vec2_Y','vec2_Z','vec2_U','vec2_V','vec2_W',C2,'vec2_F','vec2_FixFlag'};
283    case 'interp2'
284        varin={'vec2_patch_X','vec2_patch_Y','vec2_patch_Z','vec2_patch0_U','vec2_patch0_V','vec2_patch0_W','','',''};
285    case 'filter2'
286        varin={'vec2_patch_X','vec2_patch_Y','vec2_patch_Z','vec2_patch_U','vec2_patch_V','vec2_patch0_W','','',''};
287end
288if testder
289     switch vel_type
290        case 'filter1'
291            varin=[varin {'vec_patch_DUDX','vec_patch_DVDX','vec_patch_DUDY','vec_patch_DVDY'}];
292        case 'filter2'
293            varin=[varin {'vec2_patch_DUDX','vec2_patch_DVDX','vec2_patch_DUDY','vec2_patch_DVDY'}];
294    end   
295end
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