source: trunk/src/calc_field.m @ 491

Last change on this file since 491 was 491, checked in by sommeria, 9 years ago

fix the the way to deal with filter fields using tps
fix the main projection plane in uvmat

File size: 16.9 KB
Line 
1
2
3%'calc_field': defines fields (velocity, vort, div...) from civx data and calculate them
4%---------------------------------------------------------------------
5% [DataOut,errormsg]=calc_field(FieldList,DataIn,Coord_interp)
6%
7% OUTPUT:
8% Scal: matlab vector representing the scalar values (length nbvec defined by var_read)
9%      if no input, Scal=list of programmed scalar names (to put in menus)
10%      if only the field name is put as input, vec_A=type of scalar, which can be:
11%                   'discrete': related to the individual velocity vectors, not interpolated by patch
12%                   'vel': scalar calculated solely from velocity components
13%                   'der': needs spatial derivatives
14%                   'var': the scalar name directly corresponds to a field name in the netcdf files
15% error: error flag
16%      error = 0; OK
17%      error = 1; the prescribed scalar cannot be read or calculated from available fields
18%
19% INPUT:
20% FieldList: cell array of strings representing the name(s) of the field(s) to calculate
21% DataIn: structure representing the field, as defined in check_field_srtructure.m
22% Coord_interp(:,nb_coord) optional set of coordinates to interpolate the field (use with thin plate shell)
23%
24% FUNCTION related
25% varname_generator.m: determines the field names to read in the netcdf
26% file, depending on the scalar
27
28function [DataOut,errormsg]=calc_field(FieldList,DataIn,Coord_interp)
29
30%list of defined scalars to display in menus (in addition to 'ima_cor').
31% a type is associated to each scalar:
32%              'discrete': related to the individual velocity vectors, not interpolated by patch
33%              'vel': calculated from velocity components, continuous field (interpolated with velocity)
34%              'der': needs spatial derivatives
35%              'var': the scalar name corresponds to a field name in the netcdf files
36% a specific variable name for civ1 and civ2 fields are also associated, if
37% the scalar is calculated from other fields, as explicited below
38
39%% list of field options implemented
40FieldOptions={'velocity';...%image correlation corresponding to a vel vector
41    'ima_cor';...%image correlation corresponding to a vel vector
42    'norm_vel';...%norm of the velocity
43    'vort';...%vorticity
44    'div';...%divergence
45    'strain';...%rate of strain
46    'u';... %u velocity component
47    'v';... %v velocity component
48    'w';... %w velocity component
49    'w_normal';... %w velocity component normal to the plane
50    'error'}; %error associated to a vector (for stereo or patch)
51errormsg=[]; %default error message
52if ~exist('FieldList','var')
53    DataOut=FieldOptions;% gives the list of possible field inputs in the absence of input
54    return
55end
56
57%% check input
58if ~exist('DataIn','var')
59    DataIn=[];
60end
61if ischar(FieldList)
62    FieldList={FieldList};%convert a string input to a cell with one string element
63end
64check_grid=0;
65check_der=0;
66check_calc=ones(size(FieldList));
67for ilist=1:length(FieldList)
68    switch FieldList{ilist}
69        case {'u','v','velocity','norm_vel','ima_cor'}
70            check_grid=1;% needs a regular grid
71        case{'vort','div','strain'}% needs spatial derivatives spatial derivatives
72            check_der=1;
73%         case {'velocity','norm_vel','ima_cor'};
74        otherwise
75            check_calc(ilist)=0;
76    end
77end
78FieldList=FieldList(check_calc==1);
79% if isempty(FieldList)
80%     DataOut=DataIn;
81%     return
82% end
83if isfield(DataIn,'Z')&& isequal(size(DataIn.Z),size(DataIn.X))
84    nbcoord=3;
85else
86    nbcoord=2;
87end
88ListVarName={};
89ValueList={};
90RoleList={};
91units_cell={};
92
93%% interpolation with new civ data
94if isfield(DataIn,'SubRange') && isfield(DataIn,'Coord_tps') && (exist('Coord_interp','var') || check_grid ||check_der)
95    %reproduce global attributes
96    DataOut.ListGlobalAttribute=DataIn.ListGlobalAttribute;
97    for ilist=1:numel(DataOut.ListGlobalAttribute)
98        DataOut.(DataOut.ListGlobalAttribute{ilist})=DataIn.(DataIn.ListGlobalAttribute{ilist});
99    end
100
101    %create a default grid if needed
102    if  ~exist('Coord_interp','var')
103            XMax=max(max(DataIn.SubRange(1,:,:)));% extrema of the coordinates
104            YMax=max(max(DataIn.SubRange(2,:,:)));
105            XMin=min(min(DataIn.SubRange(1,:,:)));
106            YMin=min(min(DataIn.SubRange(2,:,:)));
107        if ~isfield(DataIn,'Mesh')
108            DataIn.Mesh=sqrt(2*(XMax-XMin)*(YMax-YMin)/numel(DataIn.Coord_tps));
109            % adjust the mesh to a value 1, 2 , 5 *10^n
110            ord=10^(floor(log10(DataIn.Mesh)));%order of magnitude
111            if DataIn.Mesh/ord>=5
112                DataIn.Mesh=5*ord;
113            elseif DataIn.Mesh/ord>=2
114                DataIn.Mesh=2*ord;
115            else
116                DataIn.Mesh=ord;
117            end
118        end
119        coord_x=XMin:DataIn.Mesh:XMax;
120        coord_y=YMin:DataIn.Mesh:YMax;
121%         npx=length(coord_x);
122%         npy=length(coord_y);
123        DataOut.coord_x=[XMin XMax];
124        DataOut.coord_y=[YMin YMax];
125        [XI,YI]=meshgrid(coord_x,coord_y);
126%         XI=reshape(XI,[],1);
127%         YI=reshape(YI,[],1);
128        Coord_interp=cat(3,XI,YI);%[XI YI];
129    end
130    npx=size(Coord_interp,2);
131    npy=size(Coord_interp,1);
132    Coord_interp=reshape(Coord_interp,npx*npy,size(Coord_interp,3));
133%         npy=length(coord_y);
134    %initialise output
135    nb_sites=size(Coord_interp,1);
136    nb_coord=size(Coord_interp,2);
137    nbval=zeros(nb_sites,1);
138    NbSubDomain=size(DataIn.SubRange,3);
139    DataOut.ListVarName={'coord_y','coord_x'};
140    DataOut.VarDimName={{'coord_y'},{'coord_x'}};
141    DataOut.VarAttribute{1}=[];
142    DataOut.VarAttribute{2}=[];
143    for ilist=1:length(FieldList)
144        switch FieldList{ilist}
145            case 'velocity'
146                DataOut.U=zeros(nb_sites,1);
147                DataOut.V=zeros(nb_sites,1);
148            otherwise
149                DataOut.(FieldList{ilist})=zeros(nb_sites,1);
150        end
151    end
152   
153    % interpolate data in each subdomain
154    for isub=1:NbSubDomain
155        nbvec_sub=DataIn.NbSites(isub);
156        check_range=(Coord_interp >=ones(nb_sites,1)*DataIn.SubRange(:,1,isub)' & Coord_interp<=ones(nb_sites,1)*DataIn.SubRange(:,2,isub)');
157        ind_sel=find(sum(check_range,2)==nb_coord);
158        %rho smoothing parameter
159        %                 epoints = Coord_interp(ind_sel) ;% coordinates of interpolation sites
160        %                 ctrs=DataIn.Coord_tps(1:nbvec_sub,:,isub);%(=initial points) ctrs
161        nbval(ind_sel)=nbval(ind_sel)+1;% records the number of values for eacn interpolation point (in case of subdomain overlap)
162        if check_grid
163            EM = tps_eval(Coord_interp(ind_sel,:),DataIn.Coord_tps(1:nbvec_sub,:,isub));%kernels for calculating the velocity from tps 'sources'
164        end
165        if check_der
166            [EMDX,EMDY] = tps_eval_dxy(Coord_interp(ind_sel,:),DataIn.Coord_tps(1:nbvec_sub,:,isub));%kernels for calculating the spatial derivatives from tps 'sources'
167        end
168        ListVar={};
169        for ilist=1:length(FieldList)
170            var_count=numel(ListVar);
171            switch FieldList{ilist}
172                case 'velocity'
173                    ListVar=[ListVar {'U', 'V'}];
174                    VarAttribute{var_count+1}.Role='vector_x';
175                    VarAttribute{var_count+2}.Role='vector_y';
176                    DataOut.U(ind_sel)=DataOut.U(ind_sel)+EM *DataIn.U_tps(1:nbvec_sub+3,isub);
177                    DataOut.V(ind_sel)=DataOut.V(ind_sel)+EM *DataIn.V_tps(1:nbvec_sub+3,isub);
178                case 'u'
179                    ListVar=[ListVar {'u'}];
180                    VarAttribute{var_count+1}.Role='scalar';
181                    DataOut.u(ind_sel)=DataOut.u(ind_sel)+EM *DataIn.U_tps(1:nbvec_sub+3,isub);
182                case 'v'
183                    ListVar=[ListVar {'v'}];
184                    VarAttribute{var_count+1}.Role='scalar';
185                    DataOut.v(ind_sel)=DataOut.v(ind_sel)+EM *DataIn.V_tps(1:nbvec_sub+3,isub);
186                case 'norm_vel'
187                    ListVar=[ListVar {'norm_vel'}];
188                    VarAttribute{var_count+1}.Role='scalar';
189                    U=DataOut.U(ind_sel)+EM *DataIn.U_tps(1:nbvec_sub+3,isub);
190                    V=DataOut.V(ind_sel)+EM *DataIn.V_tps(1:nbvec_sub+3,isub);
191                    DataOut.norm_vel(ind_sel)=sqrt(U.*U+V.*V);
192                case 'vort'
193                    ListVar=[ListVar {'vort'}];
194                    VarAttribute{var_count+1}.Role='scalar';
195                    DataOut.vort(ind_sel)=DataOut.vort(ind_sel)-EMDY *DataIn.U_tps(1:nbvec_sub+3,isub)+EMDX *DataIn.V_tps(1:nbvec_sub+3,isub);
196                case 'div'
197                    ListVar=[ListVar {'div'}];
198                    VarAttribute{var_count+1}.Role='scalar';
199                    DataOut.div(ind_sel)=DataOut.div(ind_sel)+EMDX*DataIn.U_tps(1:nbvec_sub+3,isub)+EMDY *DataIn.V_tps(1:nbvec_sub+3,isub);
200                case 'strain'
201                    ListVar=[ListVar {'strain'}];
202                    VarAttribute{var_count+1}.Role='scalar';
203                    DataOut.strain(ind_sel)=DataOut.strain(ind_sel)+EMDY*DataIn.U_tps(1:nbvec_sub+3,isub)+EMDX *DataIn.V_tps(1:nbvec_sub+3,isub);
204            end
205        end
206    end
207    DataOut.FF=nbval==0; %put errorflag to 1 for points outside the interpolation rang
208    nbval(nbval==0)=1;% to avoid division by zero for averaging
209    if isempty(find(strcmp('FF',DataOut.ListVarName),1))% if FF is not already listed
210        DataOut.ListVarName=[DataOut.ListVarName {'FF'}];
211        DataOut.VarDimName=[DataOut.VarDimName {{'coord_y','coord_x'}}];
212        DataOut.VarAttribute{length(DataOut.ListVarName)}.Role='errorflag';
213    end
214    DataOut.ListVarName=[DataOut.ListVarName ListVar];
215    for ifield=1:numel(ListVar)
216        VarDimName{ifield}={'coord_y','coord_x'};
217        DataOut.(ListVar{ifield})=DataOut.(ListVar{ifield})./nbval;
218        DataOut.(ListVar{ifield})=reshape(DataOut.(ListVar{ifield}),npy,npx);
219    end
220    DataOut.FF=reshape(DataOut.FF,npy,npx);
221    DataOut.VarDimName=[DataOut.VarDimName VarDimName];     
222    DataOut.VarAttribute=[DataOut.VarAttribute VarAttribute];
223else
224
225    %% civx data
226    DataOut=DataIn;
227    for ilist=1:length(FieldList)
228        if ~isempty(FieldList{ilist})
229            [VarName,Value,Role,units]=feval(FieldList{ilist},DataIn);%calculate field with appropriate function named FieldList{ilist}
230            ListVarName=[ListVarName VarName];
231            ValueList=[ValueList Value];
232            RoleList=[RoleList Role];
233            units_cell=[units_cell units];
234        end
235    end
236    %erase previous data (except coordinates)
237    for ivar=nbcoord+1:length(DataOut.ListVarName)
238        VarName=DataOut.ListVarName{ivar};
239        DataOut=rmfield(DataOut,VarName);
240    end
241    DataOut.ListVarName=DataOut.ListVarName(1:nbcoord);
242    if isfield(DataOut,'VarDimName')
243        DataOut.VarDimName=DataOut.VarDimName(1:nbcoord);
244    else
245        errormsg='element .VarDimName missing in input data';
246        return
247    end
248    DataOut.VarAttribute=DataOut.VarAttribute(1:nbcoord);
249    %append new data
250    DataOut.ListVarName=[DataOut.ListVarName ListVarName];
251    for ivar=1:length(ListVarName)
252        DataOut.VarDimName{nbcoord+ivar}=DataOut.VarDimName{1};
253        DataOut.VarAttribute{nbcoord+ivar}.Role=RoleList{ivar};
254        DataOut.VarAttribute{nbcoord+ivar}.units=units_cell{ivar};
255        DataOut.(ListVarName{ivar})=ValueList{ivar};
256    end
257end
258
259
260
261%%%%%%%%%%%%% velocity fieldn%%%%%%%%%%%%%%%%%%%%
262function [VarName,ValCell,Role,units_cell]=velocity(DataIn)
263VarName={};
264ValCell={};
265Role={};
266units_cell={};
267if isfield(DataIn,'CoordUnit') && isfield(DataIn,'TimeUnit')
268    units=[DataIn.CoordUnit '/' DataIn.TimeUnit];
269else
270    units='pixel';
271end
272if isfield(DataIn,'U')
273    VarName=[VarName {'U'}];
274    ValCell=[ValCell {DataIn.U}];
275    Role=[Role {'vector_x'}];
276    units_cell=[units_cell {units}];
277end
278if isfield(DataIn,'V')
279    VarName=[VarName {'V'}];
280    ValCell=[ValCell {DataIn.V}];
281    Role=[Role {'vector_y'}];
282    units_cell=[units_cell {units}];
283end
284if isfield(DataIn,'W')
285    VarName=[VarName {'W'}];
286    ValCell=[ValCell {DataIn.W}];
287    Role=[Role {'vector_z'}];
288    units_cell=[units_cell {units}];
289end
290if isfield(DataIn,'F')
291    VarName=[VarName {'F'}];
292    ValCell=[ValCell {DataIn.F}];
293    Role=[Role {'warnflag'}];
294    units_cell=[units_cell {[]}];
295end
296if isfield(DataIn,'FF')
297    VarName=[VarName,{'FF'}];
298    ValCell=[ValCell {DataIn.FF}];
299    Role=[Role {'errorflag'}];
300    units_cell=[units_cell {[]}];
301end
302
303%%%%%%%%%%%%% ima cor%%%%%%%%%%%%%%%%%%%%
304function [VarName,ValCell,Role,units]=ima_cor(DataIn)
305VarName={};
306ValCell={};
307Role={};
308units={};
309if isfield(DataIn,'C')
310    VarName{1}='C';
311    ValCell{1}=DataIn.C;
312    Role={'ancillary'};
313    units={[]};
314end
315
316%%%%%%%%%%%%% norm_vec %%%%%%%%%%%%%%%%%%%%
317function [VarName,ValCell,Role,units]=norm_vel(DataIn)
318VarName={};
319ValCell={};
320Role={};
321units={};
322if isfield(DataIn,'U') && isfield(DataIn,'V')
323    VarName{1}='norm_vel';
324    ValCell{1}=DataIn.U.*DataIn.U+ DataIn.V.*DataIn.V;
325    if isfield(DataIn,'W') && isequal(size(DataIn.W),size(DataIn.U))
326        ValCell{1}=ValCell{1}+DataIn.W.*DataIn.W;
327    end
328    ValCell{1}=sqrt(ValCell{1});
329    Role{1}='scalar';
330    if isfield(DataIn,'CoordUnit') && isfield(DataIn,'TimeUnit')
331        units={[DataIn.CoordUnit '/' DataIn.TimeUnit]};
332    else
333        units={'pixel'};
334    end
335end
336
337
338
339%%%%%%%%%%%%% vorticity%%%%%%%%%%%%%%%%%%%%
340function [VarName,ValCell,Role,units]=vort(DataIn)
341VarName={};
342ValCell={};
343Role={};
344units={};
345if isfield(DataIn,'DjUi')
346    VarName{1}='vort';
347    ValCell{1}=DataIn.DjUi(:,1,2)-DataIn.DjUi(:,2,1);  %vorticity
348    siz=size(ValCell{1});
349    ValCell{1}=reshape(ValCell{1},siz(1),1);
350    Role{1}='scalar';
351    if isfield(DataIn,'TimeUnit')
352        units={[DataIn.TimeUnit '-1']};
353    else
354        units={[]};
355    end
356end
357
358%%%%%%%%%%%%% divergence%%%%%%%%%%%%%%%%%%%%
359function [VarName,ValCell,Role,units]=div(DataIn)
360VarName={};
361ValCell={};
362Role={};
363units={};
364if isfield(DataIn,'DjUi')
365    VarName{1}='div';
366    ValCell{1}=DataIn.DjUi(:,1,1)+DataIn.DjUi(:,2,2); %DUDX+DVDY
367    siz=size(ValCell{1});
368    ValCell{1}=reshape(ValCell{1},siz(1),1);
369    Role{1}='scalar';
370    if isfield(DataIn,'TimeUnit')
371        units={[DataIn.TimeUnit '-1']};
372    else
373        units={[]};
374    end
375end
376
377%%%%%%%%%%%%% strain %%%%%%%%%%%%%%%%%%%%
378function [VarName,ValCell,Role,units]=strain(DataIn)
379VarName={};
380ValCell={};
381Role={};
382units={};
383if isfield(DataIn,'DjUi')
384    VarName{1}='strain';
385    ValCell{1}=DataIn.DjUi(:,1,2)+DataIn.DjUi(:,2,1);%DVDX+DUDY
386    siz=size(ValCell{1});
387    ValCell{1}=reshape(ValCell{1},siz(1),1);
388    Role{1}='scalar';
389    if isfield(DataIn,'TimeUnit')
390        units={[DataIn.TimeUnit '-1']};
391    else
392        units={[]};
393    end
394end
395
396%%%%%%%%%%%%% u %%%%%%%%%%%%%%%%%%%%
397function [VarName,ValCell,Role,units]=u(DataIn)
398VarName={};
399ValCell={};
400Role={};
401units={};
402if isfield(DataIn,'U')
403    VarName{1}='U';
404    ValCell{1}=DataIn.U;
405    Role{1}='scalar';
406    if isfield(DataIn,'CoordUnit') && isfield(DataIn,'TimeUnit')
407        units={[DataIn.CoordUnit '/' DataIn.TimeUnit]};
408    else
409        units={'pixel'};
410    end
411end
412
413%%%%%%%%%%%%% v %%%%%%%%%%%%%%%%%%%%
414function [VarName,ValCell,Role,units]=v(DataIn)
415VarName={};
416ValCell={};
417Role={};
418units={};
419if isfield(DataIn,'V')
420    VarName{1}='V';
421    ValCell{1}=DataIn.V;
422    Role{1}='scalar';
423    if isfield(DataIn,'CoordUnit') && isfield(DataIn,'TimeUnit')
424        units={[DataIn.CoordUnit '/' DataIn.TimeUnit]};
425    else
426        units={'pixel'};
427    end
428end
429
430%%%%%%%%%%%%% w %%%%%%%%%%%%%%%%%%%%
431function [VarName,ValCell,Role,units]=w(DataIn)
432VarName={};
433ValCell={};
434Role={};
435units={};
436if isfield(DataIn,'W')
437    VarName{1}='W';
438    ValCell{1}=DataIn.W;
439    Role{1}='scalar';%will remain unchanged by projection
440    if isfield(DataIn,'CoordUnit') && isfield(DataIn,'TimeUnit')
441        units={[DataIn.CoordUnit '/' DataIn.TimeUnit]};
442    else
443        units={'pixel'};
444    end
445end
446
447%%%%%%%%%%%%% w_normal %%%%%%%%%%%%%%%%%%%%
448function [VarName,ValCell,Role,units]=w_normal(DataIn)
449VarName={};
450ValCell={};
451Role={};
452units={};
453if isfield(DataIn,'W')
454    VarName{1}='W';
455    ValCell{1}=DataIn.W;
456    Role{1}='vector_z';%will behave like a vector component  by projection
457    if isfield(DataIn,'CoordUnit') && isfield(DataIn,'TimeUnit')
458        units={[DataIn.CoordUnit '/' DataIn.TimeUnit]};
459    else
460        units={'pixel'};
461    end
462end
463
464%%%%%%%%%%%%% error %%%%%%%%%%%%%%%%%%%%
465function [VarName,ValCell,Role,units]=error(DataIn)
466VarName={};
467ValCell={};
468Role={};
469units={};
470if isfield(DataIn,'E')
471    VarName{1}='E';
472    ValCell{1}=DataIn.E;
473    Role{1}='ancillary'; %TODO CHECK units in actual fields
474    if isfield(DataIn,'CoordUnit') && isfield(DataIn,'TimeUnit')
475        units={[DataIn.CoordUnit '/' DataIn.TimeUnit]};
476    else
477        units={'pixel'};
478    end
479end
480
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