source: trunk/src/series/civ2vel_3C.m @ 1027

Last change on this file since 1027 was 1027, checked in by g7moreau, 3 years ago
  • Update Copyright 2017 -> 2018
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1%'civ2vel_3C': combine velocity fields from two cameras to get three velocity components
2%------------------------------------------------------------------------
3% function ParamOut=civ2vel_3C(Param)
4%
5%OUTPUT
6% ParamOut: sets options in the GUI series.fig needed for the function
7%
8%INPUT:
9% In run mode, the input parameters are given as a Matlab structure Param copied from the GUI series.
10% In batch mode, Param is the name of the corresponding xml file containing the same information
11% when Param.Action.RUN=0 (as activated when the current Action is selected
12% in series), the function ouput paramOut set the activation of the needed GUI elements
13%
14% Param contains the elements:(use the menu bar command 'export/GUI config' in series to
15% see the current structure Param)
16%    .InputTable: cell of input file names, (several lines for multiple input)
17%                      each line decomposed as {RootPath,SubDir,Rootfile,NomType,Extension}
18%    .OutputSubDir: name of the subdirectory for data outputs
19%    .OutputDirExt: directory extension for data outputs
20%    .Action: .ActionName: name of the current activated function
21%             .ActionPath:   path of the current activated function
22%             .ActionExt: fct extension ('.m', Matlab fct, '.sh', compiled   Matlab fct
23%             .RUN =0 for GUI input, =1 for function activation
24%             .RunMode='local','background', 'cluster': type of function  use
25%             
26%    .IndexRange: set the file or frame indices on which the action must be performed
27%    .InputFields: sub structure describing the input fields withfields
28%              .FieldName: name(s) of the field
29%              .VelType: velocity type
30%              .FieldName_1: name of the second field in case of two input series
31%              .VelType_1: velocity type of the second field in case of two input series
32%              .Coord_y: name of y coordinate variable
33%              .Coord_x: name of x coordinate variable'
34
35%=======================================================================
36% Copyright 2008-2018, LEGI UMR 5519 / CNRS UGA G-INP, Grenoble, France
37%   http://www.legi.grenoble-inp.fr
38%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
39%
40%     This file is part of the toolbox UVMAT.
41%
42%     UVMAT is free software; you can redistribute it and/or modify
43%     it under the terms of the GNU General Public License as published
44%     by the Free Software Foundation; either version 2 of the license,
45%     or (at your option) any later version.
46%
47%     UVMAT is distributed in the hope that it will be useful,
48%     but WITHOUT ANY WARRANTY; without even the implied warranty of
49%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
50%     GNU General Public License (see LICENSE.txt) for more details.
51%=======================================================================
52
53function ParamOut=civ2vel_3C(Param)
54disp('test')
55%% set the input elements needed on the GUI series when the function is selected in the menu ActionName or InputTable refreshed
56if isstruct(Param) && isequal(Param.Action.RUN,0)
57    ParamOut.AllowInputSort='off';% allow alphabetic sorting of the list of input file SubDir (options 'off'/'on', 'off' by default)
58    ParamOut.WholeIndexRange='off';% prescribes the file index ranges from min to max (options 'off'/'on', 'off' by default)
59    ParamOut.NbSlice='off'; %nbre of slices ('off' by default)
60    ParamOut.VelType='one';% menu for selecting the velocity type (options 'off'/'one'/'two',  'off' by default)
61    ParamOut.FieldName='off';% menu for selecting the field (s) in the input file(options 'off'/'one'/'two', 'off' by default)
62    ParamOut.FieldTransform = 'off';%use the phys  transform function without choice
63    %ParamOut.TransformPath=fullfile(fileparts(which('uvmat')),'transform_field');% path to transform functions (needed for compilation only)
64    ParamOut.ProjObject='on';%can use projection object(option 'off'/'on',
65    ParamOut.Mask='off';%can use mask option   (option 'off'/'on', 'off' by default)
66    ParamOut.OutputDirExt='.vel3C';%set the output dir extension
67    ParamOut.OutputSubDirMode='two'; % the two first input lines are used to define the output subfolder
68    ParamOut.OutputFileMode='NbInput';% '=NbInput': 1 output file per input file index, '=NbInput_i': 1 file per input file index i, '=NbSlice': 1 file per slice
69    %check the input files
70    ParamOut.CheckOverwriteVisible='on'; % manage the overwrite of existing files (default=1)
71    first_j=[];
72    if size(Param.InputTable,1)<2
73        msgbox_uvmat('WARNING',['two or three input file series are needed'])
74    end
75    if isfield(Param.IndexRange,'first_j'); first_j=Param.IndexRange.first_j; end
76    PairString='';
77    if isfield(Param.IndexRange,'PairString'); PairString=Param.IndexRange.PairString; end
78    [i1,i2,j1,j2] = get_file_index(Param.IndexRange.first_i,first_j,PairString);
79    FirstFileName=fullfile_uvmat(Param.InputTable{1,1},Param.InputTable{1,2},Param.InputTable{1,3},...
80        Param.InputTable{1,5},Param.InputTable{1,4},i1,i2,j1,j2);
81    if ~exist(FirstFileName,'file')
82        msgbox_uvmat('WARNING',['the first input file ' FirstFileName ' does not exist'])
83    elseif isequal(size(Param.InputTable,1),1) && ~isfield(Param,'ProjObject')
84        msgbox_uvmat('WARNING','You may need a projection object of type plane for merge_proj')
85    end
86    return
87end
88
89%%%%%%%%%%%% STANDARD PART (DO NOT EDIT) %%%%%%%%%%%%
90ParamOut=[]; %default output
91%% read input parameters from an xml file if input is a file name (batch mode)
92checkrun=1;
93if ischar(Param)
94    Param=xml2struct(Param);% read Param as input file (batch case)
95    checkrun=0;
96end
97hseries=findobj(allchild(0),'Tag','series');
98RUNHandle=findobj(hseries,'Tag','RUN');%handle of RUN button in GUI series
99WaitbarHandle=findobj(hseries,'Tag','Waitbar');%handle of waitbar in GUI series
100
101
102%% root input file(s) name, type and index series
103RootPath=Param.InputTable(:,1);
104RootFile=Param.InputTable(:,3);
105SubDir=Param.InputTable(:,2);
106NomType=Param.InputTable(:,4);
107FileExt=Param.InputTable(:,5);
108hdisp=disp_uvmat('WAITING...','checking the file series',checkrun);
109[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
110if ~isempty(hdisp),delete(hdisp),end;
111%%%%%%%%%%%%
112% The cell array filecell is the list of input file names, while
113% filecell{iview,fileindex}:
114%        iview: line in the table corresponding to a given file series
115%        fileindex: file index within  the file series,
116% i1_series(iview,ref_j,ref_i)... are the corresponding arrays of indices i1,i2,j1,j2, depending on the input line iview and the two reference indices ref_i,ref_j
117% i1_series(iview,fileindex) expresses the same indices as a 1D array in file indices
118%%%%%%%%%%%%
119NbView=numel(i1_series);%number of input file series (lines in InputTable)
120NbField_j=size(i1_series{1},1); %nb of fields for the j index (bursts or volume slices)
121NbField_i=size(i1_series{1},2); %nb of fields for the i index
122NbField=NbField_j*NbField_i; %total number of fields
123
124%% define the directory for result file (with path=RootPath{1})
125OutputDir=[Param.OutputSubDir Param.OutputDirExt];% subdirectory for output files
126%
127% if ~isfield(Param,'InputFields')
128%     Param.InputFields.FieldName='';
129% end
130
131%% calibration data and timing: read the ImaDoc files
132[XmlData,NbSlice_calib,time,errormsg]=read_multimadoc(RootPath,SubDir,RootFile,FileExt,i1_series,i2_series,j1_series,j2_series);
133if size(time,1)>1
134    diff_time=max(max(diff(time)));
135    if diff_time>0
136        disp_uvmat('WARNING',['times of series differ by (max) ' num2str(diff_time) ': the mean time is chosen in result'],checkrun)
137    end
138end
139if ~isempty(errormsg)
140    disp_uvmat('WARNING',errormsg,checkrun)
141end
142time=mean(time,1); %averaged time taken for the merged field
143if isfield(XmlData{1},'GeometryCalib')
144    tsaiA=XmlData{1}.GeometryCalib;
145else
146    disp_uvmat('ERROR','no geometric calibration available for image A',checkrun)
147    return
148end
149if isfield(XmlData{2},'GeometryCalib')
150    tsaiB=XmlData{2}.GeometryCalib;
151else
152    disp_uvmat('ERROR','no geometric calibration available for image B',checkrun)
153    return
154end
155[filecell,i1_series,i2_series,j1_series,j2_series]=get_file_series(Param);
156
157%% grid of physical positions (given by projection plane)
158if ~Param.CheckObject
159    disp_uvmat('ERROR','a projection plane with interpolation is needed',checkrun)
160    return
161end
162ObjectData=Param.ProjObject;
163xI=ObjectData.RangeX(1):ObjectData.DX:ObjectData.RangeX(2);
164yI=ObjectData.RangeY(1):ObjectData.DY:ObjectData.RangeY(2);
165[XI,YI]=meshgrid(xI,yI);
166U=zeros(size(XI,1),size(XI,2));
167V=zeros(size(XI,1),size(XI,2));
168W=zeros(size(XI,1),size(XI,2));
169
170%% MAIN LOOP ON FIELDS
171warning off
172
173CheckOverwrite=1;%default
174if isfield(Param,'CheckOverwrite')
175    CheckOverwrite=Param.CheckOverwrite;
176end
177for index=1:NbField
178   
179    update_waitbar(WaitbarHandle,index/NbField)
180   
181   
182   
183   
184      %% generating the name of the merged field
185    i1=i1_series{1}(index);
186    if ~isempty(i2_series{end})
187        i2=i2_series{end}(index);
188    else
189        i2=i1;
190    end
191    j1=1;
192    j2=1;
193    if ~isempty(j1_series{1})
194        j1=j1_series{1}(index);
195        if ~isempty(j2_series{end})
196            j2=j2_series{end}(index);
197        else
198            j2=j1;
199        end
200    end
201    OutputFile=fullfile_uvmat(RootPath{1},OutputDir,RootFile{1},'.nc','_1-2',i1,i2,j1,j2);
202   
203    %%
204   
205   
206    if ~isempty(RUNHandle) && ~strcmp(get(RUNHandle,'BusyAction'),'queue')
207        disp('program stopped by user')
208        return
209    end
210   
211     if (~CheckOverwrite && exist(OutputFile,'file')) 
212            disp('existing output file already exists, skip to next field')
213            continue% skip iteration if the mode overwrite is desactivated and the result file already exists
214     end   
215     
216    %%%%%%%%%%%%%%%% loop on views (input lines) %%%%%%%%%%%%%%%%
217    Data=cell(1,NbView);%initiate the set Data
218    timeread=zeros(1,NbView);
219   
220    %get Xphys,Yphys,Zphys from 1 or 2 stereo folders. Positions are taken
221    %at the middle between to time step
222   clear ZItemp
223   ZItemp=zeros(size(XI,1),size(XI,2),2);
224   
225   if index==1
226        first_img=i1_series{1,1}(1,1); %id of the first image of the series
227   end
228     
229     idtemp=0;
230 for indextemp=index:index+1;
231     idtemp=idtemp+1;
232    if NbView==3 % if there is only 1 stereo folder, extract directly Xphys,Yphys and Zphys
233     
234       
235       
236        [Data{3},tild,errormsg] = nc2struct([Param.InputTable{3,1},'/',Param.InputTable{3,2},'/',Param.InputTable{3,3},'_',int2str(first_img+indextemp-1),'.nc']);
237       
238        if  exist('Data{3}.Civ3_FF','var') % FF is present, remove wrong vector
239            temp=find(Data{3}.Civ3_FF==0);
240            Zphys=Data{3}.Zphys(temp);
241            Yphys=Data{3}.Yphys(temp);
242            Xphys=Data{3}.Xphys(temp);
243        else
244            Zphys=Data{3}.Zphys;
245            Yphys=Data{3}.Yphys;
246            Xphys=Data{3}.Xphys;
247        end
248       
249       
250       
251    elseif NbView==4 % is there is 2 stereo folders, get global U and V and compute Zphys
252       
253       
254        %test if the seconde camera is the same for both folder
255        for i=3:4
256        indpt(i)=strfind(Param.InputTable{i,2},'.'); % indice of the "." is the folder name 1
257        indline(i)=strfind(Param.InputTable{i,2},'-'); % indice of the "-" is the folder name1
258        camname{i}=Param.InputTable{i,2}(indline(i)+1:indpt(i)-1);% extract the second camera name
259        end
260       
261        if strcmp(camname{3},camname{4})==0
262            disp_uvmat('ERROR','The 2 stereo folders should have the same camera for the second position',checkrun)
263            return
264        end
265       
266   
267       
268        [Data{3},tild,errormsg] = nc2struct([Param.InputTable{3,1},'/',Param.InputTable{3,2},'/',Param.InputTable{3,3},'_',int2str(first_img+indextemp-1),'.nc']);
269   
270        if exist('Data{3}.Civ3_FF','var') % if FF is present, remove wrong vector
271            temp=find(Data{3}.Civ3_FF==0);
272            Xmid3=Data{3}.Xmid(temp);
273            Ymid3=Data{3}.Ymid(temp);
274            U3=Data{3}.Uphys(temp);
275            V3=Data{3}.Vphys(temp);
276        else
277            Xmid3=Data{3}.Xmid;
278            Ymid3=Data{3}.Ymid;
279            U3=Data{3}.Uphys;
280            V3=Data{3}.Vphys;
281        end
282        %temporary gridd of merging the 2 stereos datas
283        [xq,yq] = meshgrid(min(Xmid3+(U3)/2):(max(Xmid3+(U3)/2)-min(Xmid3+(U3)/2))/128:max(Xmid3+(U3)/2),min(Ymid3+(V3)/2):(max(Ymid3+(V3)/2)-min(Ymid3+(V3)/2))/128:max(Ymid3+(V3)/2));
284       
285        %1st folder : interpolate the first camera (Dalsa1) points on the second (common) camera
286        %(Dalsa 3)
287        x3Q=griddata(Xmid3+(U3)/2,Ymid3+(V3)/2,Xmid3-(U3)/2,xq,yq);
288        y3Q=griddata(Xmid3+(U3)/2,Ymid3+(V3)/2,Ymid3-(V3)/2,xq,yq);
289       
290       
291
292         [Data{4},tild,errormsg] = nc2struct([Param.InputTable{4,1},'/',Param.InputTable{4,2},'/',Param.InputTable{4,3},'_',int2str(first_img+indextemp-1),'.nc']);
293        if exist('Data{4}.Civ3_FF','var') % if FF is present, remove wrong vector
294            temp=find(Data{4}.Civ3_FF==0);
295            Xmid4=Data{4}.Xmid(temp);
296            Ymid4=Data{4}.Ymid(temp);
297            U4=Data{4}.Uphys(temp);
298            V4=Data{4}.Vphys(temp);
299        else
300            Xmid4=Data{4}.Xmid;
301            Ymid4=Data{4}.Ymid;
302            U4=Data{4}.Uphys;
303            V4=Data{4}.Vphys;
304        end
305       
306        %2nd folder :interpolate the first camera (Dalsa2) points on the second (common) camera
307        %(Dalsa 3)
308        x4Q=griddata(Xmid4+(U4)/2,Ymid4+(V4)/2,Xmid4-(U4)/2,xq,yq);
309        y4Q=griddata(Xmid4+(U4)/2,Ymid4+(V4)/2,Ymid4-(V4)/2,xq,yq);
310       
311        xmid=reshape((x4Q+x3Q)/2,length(xq(:,1)).*length(xq(1,:)),1);
312        ymid=reshape((y4Q+y3Q)/2,length(yq(:,1)).*length(yq(1,:)),1);
313        u=reshape(x4Q-x3Q,length(xq(:,1)).*length(xq(1,:)),1);
314        v=reshape(y4Q-y3Q,length(yq(:,1)).*length(yq(1,:)),1);
315       
316       
317        [Zphys,Xphys,Yphys,error]=shift2z(xmid, ymid, u, v,XmlData); %get Xphy,Yphy and Zphys
318        %remove NaN
319        tempNaN=isnan(Zphys);tempind=find(tempNaN==1);
320        Zphys(tempind)=[];
321        Xphys(tempind)=[];
322        Yphys(tempind)=[];
323        error(tempind)=[];
324         
325    end
326   
327            if NbView>2   
328       ZItemp(:,:,idtemp)=griddata(Xphys,Yphys,Zphys,XI,YI); %interpolation on the choosen gridd
329            end
330   
331end
332    ZI=mean(ZItemp,3); %mean between two the two time step
333    Vtest=ZItemp(:,:,2)-ZItemp(:,:,1);
334   
335    [Xa,Ya]=px_XYZ(XmlData{1}.GeometryCalib,XI,YI,ZI);% set of image coordinates on view a
336    [Xb,Yb]=px_XYZ(XmlData{2}.GeometryCalib,XI,YI,ZI);% set of image coordinates on view b
337   
338   
339    for iview=1:2
340        %% reading input file(s)
341        [Data{iview},tild,errormsg]=read_civdata(filecell{iview,index},{'vec(U,V)'},'*');
342        if ~isempty(errormsg)
343            disp_uvmat('ERROR',['ERROR in civ2vel_3C/read_field/' errormsg],checkrun)
344            return
345        end
346        % get the time defined in the current file if not already defined from the xml file
347        if isfield(Data{iview},'Time')&& isequal(Data{iview}.Time,Data{1}.Time)
348            Time=Data{iview}.Time;
349        else
350            disp_uvmat('ERROR','Time undefined or not synchronous',checkrun)
351            return
352        end
353        if isfield(Data{iview},'Dt')&& isequal(Data{iview}.Dt,Data{1}.Dt)
354            Dt=Data{iview}.Dt;
355        else
356            disp_uvmat('ERROR','Dt undefined or not synchronous',checkrun)
357            return
358        end
359    end
360    %remove wrong vector 
361    if isfield(Data{1},'FF')
362        temp=find(Data{1}.FF==0);
363        X1=Data{1}.X(temp);
364        Y1=Data{1}.Y(temp);
365        U1=Data{1}.U(temp);
366        V1=Data{1}.V(temp);
367    else
368        X1=Data{1}.X;
369        Y1=Data{1}.Y;
370        U1=Data{1}.U;
371        V1=Data{1}.V;
372    end
373    Ua=griddata(X1,Y1,U1,Xa,Ya);
374    Va=griddata(X1,Y1,V1,Xa,Ya);
375    [Ua,Va,Xa,Ya]=Ud2U(XmlData{1}.GeometryCalib,Xa,Ya,Ua,Va); % convert Xd data to X
376    [A]=get_coeff(XmlData{1}.GeometryCalib,Xa,Ya,XI,YI,ZI); %get coef A~
377   
378    %remove wrong vector 
379    if isfield(Data{1},'FF')
380        temp=find(Data{2}.FF==0);
381        X2=Data{2}.X(temp);
382        Y2=Data{2}.Y(temp);
383        U2=Data{2}.U(temp);
384        V2=Data{2}.V(temp);
385    else
386        X2=Data{2}.X;
387        Y2=Data{2}.Y;
388        U2=Data{2}.U;
389        V2=Data{2}.V;
390    end
391    Ub=griddata(X2,Y2,U2,Xb,Yb);
392    Vb=griddata(X2,Y2,V2,Xb,Yb);
393    [Ub,Vb,Xb,Yb]=Ud2U(XmlData{2}.GeometryCalib,Xb,Yb,Ub,Vb); % convert Xd data to X
394   
395    [B]=get_coeff(XmlData{2}.GeometryCalib,Xb,Yb,XI,YI,ZI); %get coef B~
396   
397   
398    % System to solve
399    S=ones(size(XI,1),size(XI,2),3);
400    D=ones(size(XI,1),size(XI,2),3,3);
401
402    S(:,:,1)=A(:,:,1,1).*Ua+A(:,:,2,1).*Va+B(:,:,1,1).*Ub+B(:,:,2,1).*Vb;
403    S(:,:,2)=A(:,:,1,2).*Ua+A(:,:,2,2).*Va+B(:,:,1,2).*Ub+B(:,:,2,2).*Vb;
404    S(:,:,3)=A(:,:,1,3).*Ua+A(:,:,2,3).*Va+B(:,:,1,3).*Ub+B(:,:,2,3).*Vb;
405    D(:,:,1,1)=A(:,:,1,1).*A(:,:,1,1)+A(:,:,2,1).*A(:,:,2,1)+B(:,:,1,1).*B(:,:,1,1)+B(:,:,2,1).*B(:,:,2,1);
406    D(:,:,1,2)=A(:,:,1,1).*A(:,:,1,2)+A(:,:,2,1).*A(:,:,2,2)+B(:,:,1,1).*B(:,:,1,2)+B(:,:,2,1).*B(:,:,2,2);
407    D(:,:,1,3)=A(:,:,1,1).*A(:,:,1,3)+A(:,:,2,1).*A(:,:,2,3)+B(:,:,1,1).*B(:,:,1,3)+B(:,:,2,1).*B(:,:,2,3);
408    D(:,:,2,1)=A(:,:,1,2).*A(:,:,1,1)+A(:,:,2,2).*A(:,:,2,1)+B(:,:,1,2).*B(:,:,1,1)+B(:,:,2,2).*B(:,:,2,1);
409    D(:,:,2,2)=A(:,:,1,2).*A(:,:,1,2)+A(:,:,2,2).*A(:,:,2,2)+B(:,:,1,2).*B(:,:,1,2)+B(:,:,2,2).*B(:,:,2,2);
410    D(:,:,2,3)=A(:,:,1,2).*A(:,:,1,3)+A(:,:,2,2).*A(:,:,2,3)+B(:,:,1,2).*B(:,:,1,3)+B(:,:,2,2).*B(:,:,2,3);
411    D(:,:,3,1)=A(:,:,1,3).*A(:,:,1,1)+A(:,:,2,3).*A(:,:,2,1)+B(:,:,1,3).*B(:,:,1,1)+B(:,:,2,3).*B(:,:,2,1);
412    D(:,:,3,2)=A(:,:,1,3).*A(:,:,1,2)+A(:,:,2,3).*A(:,:,2,2)+B(:,:,1,3).*B(:,:,1,2)+B(:,:,2,3).*B(:,:,2,2);
413    D(:,:,3,3)=A(:,:,1,3).*A(:,:,1,3)+A(:,:,2,3).*A(:,:,2,3)+B(:,:,1,3).*B(:,:,1,3)+B(:,:,2,3).*B(:,:,2,3);
414    for indj=1:size(XI,1)
415        for indi=1:size(XI,2)
416            dxyz=(squeeze(D(indj,indi,:,:))*1000)\(squeeze(S(indj,indi,:))*1000); % solving...
417            U(indj,indi)=dxyz(1);
418            V(indj,indi)=dxyz(2);
419            W(indj,indi)=dxyz(3);
420        end
421    end   
422    Error=zeros(size(XI,1),size(XI,2),4);
423    Error(:,:,1)=A(:,:,1,1).*U+A(:,:,1,2).*V+A(:,:,1,3).*W-Ua;
424    Error(:,:,2)=A(:,:,2,1).*U+A(:,:,2,2).*V+A(:,:,2,3).*W-Va;
425    Error(:,:,3)=B(:,:,1,1).*U+B(:,:,1,2).*V+B(:,:,1,3).*W-Ub;
426    Error(:,:,4)=B(:,:,2,1).*U+B(:,:,2,2).*V+B(:,:,2,3).*W-Vb;
427   
428   
429
430   
431 
432   
433    %% recording the merged field
434    if index==1% initiate the structure at first index
435        MergeData.ListGlobalAttribute={'Conventions','Time','Dt'};
436        MergeData.Conventions='uvmat';
437        MergeData.Time=Time;
438        MergeData.Dt=Dt;
439        MergeData.ListVarName={'coord_x','coord_y','Z','U','V','W','Error'};
440        MergeData.VarDimName={'coord_x','coord_y',{'coord_y','coord_x'},{'coord_y','coord_x'}...
441                {'coord_y','coord_x'},{'coord_y','coord_x'},{'coord_y','coord_x'}};
442        MergeData.coord_x=xI;
443        MergeData.coord_y=yI;
444    end
445    MergeData.U=U/Dt;
446    MergeData.V=V/Dt;
447    MergeData.W=W/Dt;
448    MergeData.Z=ZI;
449   
450%     mfx=(XmlData{1}.GeometryCalib.fx_fy(1)+XmlData{2}.GeometryCalib.fx_fy(1))/2;
451%     mfy=(XmlData{1}.GeometryCalib.fx_fy(2)+XmlData{2}.GeometryCalib.fx_fy(2))/2;
452    MergeData.Error=0.5*sqrt(sum(Error.^2,3));
453    errormsg=struct2nc(OutputFile,MergeData);%save result file
454    if isempty(errormsg)
455        disp(['output file ' OutputFile ' written'])
456    else
457        disp(errormsg)
458    end
459end
460
461
462function [A]=get_coeff(Calib,X,Y,x,y,z) % compute A~ coefficients
463R=(Calib.R)';%rotation matrix
464T_z=Calib.Tx_Ty_Tz(3);
465T=R(7)*x+R(8)*y+R(9)*z+T_z;
466
467A(:,:,1,1)=(R(1)-R(7)*X)./T;
468A(:,:,1,2)=(R(2)-R(8)*X)./T;
469A(:,:,1,3)=(R(3)-R(9)*X)./T;
470A(:,:,2,1)=(R(4)-R(7)*Y)./T;
471A(:,:,2,2)=(R(5)-R(8)*Y)./T;
472A(:,:,2,3)=(R(6)-R(9)*Y)./T;
473
474function [U,V,X,Y]=Ud2U(Calib,Xd,Yd,Ud,Vd) % convert Xd to X  and Ud to U
475
476X1d=Xd-Ud/2;
477X2d=Xd+Ud/2;
478Y1d=Yd-Vd/2;
479Y2d=Yd+Vd/2;
480
481X1=(X1d-Calib.Cx_Cy(1))./Calib.fx_fy(1).*(1 + Calib.kc.*Calib.fx_fy(1).^(-2).*(X1d-Calib.Cx_Cy(1)).^2 + Calib.kc.*Calib.fx_fy(2).^(-2).*(Y1d-Calib.Cx_Cy(2)).^2 ).^(-1);
482X2=(X2d-Calib.Cx_Cy(1))./Calib.fx_fy(1).*(1 + Calib.kc.*Calib.fx_fy(1).^(-2).*(X2d-Calib.Cx_Cy(1)).^2 + Calib.kc.*Calib.fx_fy(2).^(-2).*(Y2d-Calib.Cx_Cy(2)).^2 ).^(-1);
483Y1=(Y1d-Calib.Cx_Cy(2))./Calib.fx_fy(2).*(1 + Calib.kc.*Calib.fx_fy(1).^(-2).*(X1d-Calib.Cx_Cy(1)).^2 + Calib.kc.*Calib.fx_fy(2).^(-2).*(Y1d-Calib.Cx_Cy(2)).^2 ).^(-1);
484Y2=(Y2d-Calib.Cx_Cy(2))./Calib.fx_fy(2).*(1 + Calib.kc.*Calib.fx_fy(1).^(-2).*(X2d-Calib.Cx_Cy(1)).^2 + Calib.kc.*Calib.fx_fy(2).^(-2).*(Y2d-Calib.Cx_Cy(2)).^2 ).^(-1);
485
486U=X2-X1;
487V=Y2-Y1;
488X=X1+U/2;
489Y=Y1+V/2;
490
491
492
493function [z,Xphy,Yphy,error]=shift2z(xmid, ymid, u, v,XmlData) % get H from stereo data
494z=0;
495error=0;
496
497
498%% first image
499Calib_A=XmlData{1}.GeometryCalib;
500R=(Calib_A.R)';
501x_a=xmid- u/2;
502y_a=ymid- v/2;
503z_a=R(7)*x_a+R(8)*y_a+Calib_A.Tx_Ty_Tz(1,3);
504Xa=(R(1)*x_a+R(2)*y_a+Calib_A.Tx_Ty_Tz(1,1))./z_a;
505Ya=(R(4)*x_a+R(5)*y_a+Calib_A.Tx_Ty_Tz(1,2))./z_a;
506
507A_1_1=R(1)-R(7)*Xa;
508A_1_2=R(2)-R(8)*Xa;
509A_1_3=R(3)-R(9)*Xa;
510A_2_1=R(4)-R(7)*Ya;
511A_2_2=R(5)-R(8)*Ya;
512A_2_3=R(6)-R(9)*Ya;
513Det=A_1_1.*A_2_2-A_1_2.*A_2_1;
514Dxa=(A_1_2.*A_2_3-A_2_2.*A_1_3)./Det;
515Dya=(A_2_1.*A_1_3-A_1_1.*A_2_3)./Det;
516
517%% second image
518%loading shift angle
519
520Calib_B=XmlData{2}.GeometryCalib;
521R=(Calib_B.R)';
522
523
524x_b=xmid+ u/2;
525y_b=ymid+ v/2;
526z_b=R(7)*x_b+R(8)*y_b+Calib_B.Tx_Ty_Tz(1,3);
527Xb=(R(1)*x_b+R(2)*y_b+Calib_B.Tx_Ty_Tz(1,1))./z_b;
528Yb=(R(4)*x_b+R(5)*y_b+Calib_B.Tx_Ty_Tz(1,2))./z_b;
529B_1_1=R(1)-R(7)*Xb;
530B_1_2=R(2)-R(8)*Xb;
531B_1_3=R(3)-R(9)*Xb;
532B_2_1=R(4)-R(7)*Yb;
533B_2_2=R(5)-R(8)*Yb;
534B_2_3=R(6)-R(9)*Yb;
535Det=B_1_1.*B_2_2-B_1_2.*B_2_1;
536Dxb=(B_1_2.*B_2_3-B_2_2.*B_1_3)./Det;
537Dyb=(B_2_1.*B_1_3-B_1_1.*B_2_3)./Det;
538
539%% result
540Den=(Dxb-Dxa).*(Dxb-Dxa)+(Dyb-Dya).*(Dyb-Dya);
541error=abs(((Dyb-Dya).*(-u)-(Dxb-Dxa).*(-v)))./Den;
542% ex=-error.*(Dyb-Dya);
543% ey=-error.*(Dxb-Dxa);
544
545% z1=-u./(Dxb-Dxa);
546% z2=-v./(Dyb-Dya);
547z=((Dxb-Dxa).*(-u)+(Dyb-Dya).*(-v))./Den;
548
549xnew(1,:)=Dxa.*z+x_a;
550xnew(2,:)=Dxb.*z+x_b;
551ynew(1,:)=Dya.*z+y_a;
552ynew(2,:)=Dyb.*z+y_b;
553Xphy=mean(xnew,1);
554Yphy=mean(ynew,1);
555
556
557
558
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