source: trunk/src/transform_field/phys.m @ 167

Last change on this file since 167 was 167, checked in by sommeria, 10 years ago

small bug repair in phys and phys_polar: units

File size: 12.9 KB
Line 
1%'phys': transforms image (px) to real world (phys) coordinates using geometric calibration parameters
2% DataOut=phys(Data,CalibData) , transform one input field
3% [DataOut,DataOut_1]=phys(Data,CalibData,Data_1,CalibData_1), transform two input fields
4
5% OUTPUT:
6% DataOut:   structure representing the modified field
7% DataOut_1: structure representing the second modified field
8
9%INPUT:
10% Data:  structure of input data
11%       with fields .A (image or scalar matrix), AX, AY
12%       .X,.Y,.U,.V, .DjUi
13%       .ZIndex: index of plane in multilevel case
14%       .CoordType='phys' or 'px', The function ACTS ONLY IF .CoordType='px'
15% CalibData: structure containing calibration parameters or a subtree Calib.GeometryCalib =calibration data (tsai parameters)
16
17function [DataOut,DataOut_1]=phys(varargin)
18% A FAIRE: 1- verifier si DataIn est une 'field structure'(.ListVarName'):
19% chercher ListVarAttribute, for each field (cell of variables):
20%   .CoordType: 'phys' or 'px'   (default==phys, no transform)
21%   .scale_factor: =dt (to transform displacement into velocity) default=1
22%   .covariance: 'scalar', 'coord', 'D_i': covariant (like velocity), 'D^i': contravariant (like gradient), 'D^jD_i' (like strain tensor)
23%   (default='coord' if .Role='coord_x,_y...,
24%            'D_i' if '.Role='vector_x,...',
25%              'scalar', else (thenno change except scale factor)
26Calib{1}=[];
27if nargin==2||nargin==4 % nargin =nbre of input variables
28    Data=varargin{1};
29    DataOut=Data;%default
30    DataOut_1=[];%default
31    CalibData=varargin{2};
32    if isfield(CalibData,'GeometryCalib')
33        Calib{1}=CalibData.GeometryCalib;
34    end
35    Calib{2}=Calib{1};
36else
37    DataOut.Txt='wrong input: need two or four structures';
38end
39test_1=0;
40if nargin==4
41    test_1=1;
42    Data_1=varargin{3};
43    DataOut_1=Data_1;%default
44    CalibData_1=varargin{4};
45    if isfield(CalibData_1,'GeometryCalib')
46        Calib{2}=CalibData_1.GeometryCalib;
47    end
48end
49iscalar=0;
50if  ~isempty(Calib{1})
51    DataOut=phys_1(Data,Calib{1});
52    %case of images or scalar: in case of two input fields, we need to project the transform of on the same regular grid
53    if isfield(Data,'A') && isfield(Data,'AX') && ~isempty(Data.AX) && isfield(Data,'AY')&&...
54                                           ~isempty(Data.AY) && length(Data.A)>1
55        iscalar=1;
56        A{1}=Data.A;
57    end
58end
59%transform of X,Y coordinates for vector fields
60if isfield(Data,'ZIndex')&&~isempty(Data.ZIndex)&&~isnan(Data.ZIndex)
61    ZIndex=Data.ZIndex;
62else
63    ZIndex=1;
64end
65if test_1
66    DataOut_1=phys_1(Data_1,Calib{2});
67    if isfield(Data_1,'A')&&isfield(Data_1,'AX')&&~isempty(Data_1.AX) && isfield(Data_1,'AY')&&...
68                                       ~isempty(Data_1.AY)&&length(Data_1.A)>1
69          iscalar=iscalar+1;
70          Calib{iscalar}=Calib{2};
71          A{iscalar}=Data_1.A;
72          if isfield(Data_1,'ZIndex') && ~isequal(Data_1.ZIndex,ZIndex)
73              DataOut.Txt='inconsistent plane indexes in the two input fields';
74          end
75          if iscalar==1% case for which only the second field is a scalar
76               [A,AX,AY]=phys_Ima(A,Calib,ZIndex);
77               DataOut_1.A=A{1};
78               DataOut_1.AX=AX;
79               DataOut_1.AY=AY;
80               return
81          end
82    end
83end
84if iscalar~=0
85    [A,AX,AY]=phys_Ima(A,Calib,ZIndex);%TODO : introduire interp2_uvmat ds phys_ima
86    DataOut.A=A{1};
87    DataOut.AX=AX;
88    DataOut.AY=AY;
89    if iscalar==2
90        DataOut_1.A=A{2};
91        DataOut_1.AX=AX;
92        DataOut_1.AY=AY;
93    end
94end
95
96%------------------------------------------------
97function DataOut=phys_1(Data,Calib)
98% for icell=1:length(Data)
99
100DataOut=Data;%default
101% DataOut.CoordUnit=Calib.CoordUnit; %put flag for physical coordinates
102if isfield(Calib,'SliceCoord')
103    DataOut.PlaneCoord=Calib.SliceCoord;%to generalise for any plane
104end
105% The transform ACTS ONLY IF .CoordType='px'and Calib defined
106if isfield(Data,'CoordUnit')%&& isequal(Data.CoordType,'px')&& ~isempty(Calib)
107    if isfield(Calib,'CoordUnit')
108        DataOut.CoordUnit=Calib.CoordUnit;
109    else
110        DataOut.CoordUnit='cm'; %default
111    end
112    DataOut.TimeUnit='s';
113    %transform of X,Y coordinates for vector fields
114    if isfield(Data,'ZIndex') && ~isempty(Data.ZIndex)&&~isnan(Data.ZIndex)
115        Z=Data.ZIndex;
116    else
117        Z=0;
118    end
119    if isfield(Data,'X') &&isfield(Data,'Y')&&~isempty(Data.X) && ~isempty(Data.Y)
120        [DataOut.X,DataOut.Y,DataOut.Z]=phys_XYZ(Calib,Data.X,Data.Y,Z);
121        if isfield(Data,'U')&&isfield(Data,'V')&&~isempty(Data.U) && ~isempty(Data.V)&& isfield(Data,'dt')
122            if ~isempty(Data.dt)
123            [XOut_1,YOut_1]=phys_XYZ(Calib,Data.X-Data.U/2,Data.Y-Data.V/2,Z);
124            [XOut_2,YOut_2]=phys_XYZ(Calib,Data.X+Data.U/2,Data.Y+Data.V/2,Z);
125            DataOut.U=(XOut_2-XOut_1)/Data.dt;
126            DataOut.V=(YOut_2-YOut_1)/Data.dt;
127            end
128        end
129    end
130    %transform of an image or scalar: done in phys_ima
131     
132    %transform of spatial derivatives
133    if isfield(Data,'X') && ~isempty(Data.X) && isfield(Data,'DjUi') && ~isempty(Data.DjUi)...
134          && isfield(Data,'dt')   
135        if ~isempty(Data.dt)
136            % estimate the Jacobian matrix DXpx/DXphys
137            for ip=1:length(Data.X)
138                [Xp1,Yp1]=phys_XYZ(Calib,Data.X(ip)+0.5,Data.Y(ip),Z);
139                [Xm1,Ym1]=phys_XYZ(Calib,Data.X(ip)-0.5,Data.Y(ip),Z);
140                [Xp2,Yp2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)+0.5,Z);
141                [Xm2,Ym2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)-0.5,Z);
142            %Jacobian matrix DXpphys/DXpx
143               DjXi(1,1)=(Xp1-Xm1);
144               DjXi(2,1)=(Yp1-Ym1);
145               DjXi(1,2)=(Xp2-Xm2);
146               DjXi(2,2)=(Yp2-Ym2);
147               DjUi(:,:)=Data.DjUi(ip,:,:);
148               DjUi=(DjXi*DjUi')/DjXi;% =J-1*M*J , curvature effects (derivatives of J) neglected
149               DataOut.DjUi(ip,:,:)=DjUi';
150            end
151            DataOut.DjUi =  DataOut.DjUi/Data.dt;   %     min(Data.DjUi(:,1,1))=DUDX                         
152        end
153    end
154end
155
156%%%%%%%%%%%%%%%%%%%%
157function [A_out,Rangx,Rangy]=phys_Ima(A,CalibIn,ZIndex)
158xcorner=[];
159ycorner=[];
160npx=[];
161npy=[];
162dx=ones(1,length(A));
163dy=ones(1,length(A));
164for icell=1:length(A)
165    siz=size(A{icell});
166    npx=[npx siz(2)];
167    npy=[npy siz(1)];
168    Calib=CalibIn{icell};
169    xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordinates of corners
170    yima=[0.5 0.5 siz(1)-0.5 siz(1)-0.5];
171    [xcorner_new,ycorner_new]=phys_XYZ(Calib,xima,yima,ZIndex);%corresponding physical coordinates
172    dx(icell)=(max(xcorner_new)-min(xcorner_new))/(siz(2)-1);
173    dy(icell)=(max(ycorner_new)-min(ycorner_new))/(siz(1)-1);
174    xcorner=[xcorner xcorner_new];
175    ycorner=[ycorner ycorner_new];
176end
177Rangx(1)=min(xcorner);
178Rangx(2)=max(xcorner);
179Rangy(2)=min(ycorner);
180Rangy(1)=max(ycorner);
181test_multi=(max(npx)~=min(npx)) || (max(npy)~=min(npy)); %different image lengths
182npX=1+round((Rangx(2)-Rangx(1))/min(dx));% nbre of pixels in the new image (use the finest resolution min(dx) in the set of images)
183npY=1+round((Rangy(1)-Rangy(2))/min(dy));
184x=linspace(Rangx(1),Rangx(2),npX);
185y=linspace(Rangy(1),Rangy(2),npY);
186[X,Y]=meshgrid(x,y);%grid in physical coordiantes
187vec_B=[];
188A_out={};
189for icell=1:length(A)
190    Calib=CalibIn{icell};
191    if isfield(Calib,'R') || isfield(Calib,'kc')|| test_multi ||~isequal(Calib,CalibIn{1})% the image needs to be interpolated to the new coordinates
192        zphys=0; %default
193        if isfield(Calib,'SliceCoord') %.Z= index of plane
194           SliceCoord=Calib.SliceCoord(ZIndex,:);
195           zphys=SliceCoord(3); %to generalize for non-parallel planes
196        end
197        [XIMA,YIMA]=px_XYZ(CalibIn{icell},X,Y,zphys);% image coordinates for each point in the real space grid
198        XIMA=reshape(round(XIMA),1,npX*npY);%indices reorganized in 'line'
199        YIMA=reshape(round(YIMA),1,npX*npY);
200        flagin=XIMA>=1 & XIMA<=npx(icell) & YIMA >=1 & YIMA<=npy(icell);%flagin=1 inside the original image
201        testuint8=isa(A{icell},'uint8');
202        testuint16=isa(A{icell},'uint16');
203        if numel(siz)==2 %(B/W images)
204            vec_A=reshape(A{icell},1,npx(icell)*npy(icell));%put the original image in line
205            ind_in=find(flagin);
206            ind_out=find(~flagin);
207            ICOMB=((XIMA-1)*npy(icell)+(npy(icell)+1-YIMA));
208            ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
209            vec_B(ind_in)=vec_A(ICOMB);
210            vec_B(ind_out)=zeros(size(ind_out));
211            A_out{icell}=reshape(vec_B,npY,npX);%new image in real coordinates
212        elseif numel(siz)==3     
213            for icolor=1:siz(3)
214                vec_A=reshape(A{icell}(:,:,icolor),1,npx*npy);%put the original image in line
215                ind_in=find(flagin);
216                ind_out=find(~flagin);
217                ICOMB=((XIMA-1)*npy+(npy+1-YIMA));
218                ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
219                vec_B(ind_in)=vec_A(ICOMB);
220                vec_B(ind_out)=zeros(size(ind_out));
221                A_out{icell}(:,:,icolor)=reshape(vec_B,npy,npx);%new image in real coordinates
222            end
223        end
224        if testuint8
225            A_out{icell}=uint8(A_out{icell});
226        end
227        if testuint16
228            A_out{icell}=uint16(A_out{icell});
229        end
230    else%     
231        A_out{icell}=A{icell};%no transform
232        Rangx=[0.5 npx-0.5];%image coordiantes of corners
233        Rangy=[npy-0.5 0.5];
234        [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation
235        [xx,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,ZIndex);
236    end
237end
238
239%------------------------------------------------------------------------
240%'phys_XYZ':transforms image (px) to real world (phys) coordinates using geometric calibration parameters
241% function [Xphys,Yphys]=phys_XYZ(Calib,X,Y,Z)
242%
243%OUTPUT:
244%
245%INPUT:
246%Z: index of plane
247function [Xphys,Yphys,Zphys]=phys_XYZ(Calib,X,Y,Z)
248%------------------------------------------------------------------------
249if exist('Z','var')&& isequal(Z,round(Z))&& Z>0 && isfield(Calib,'SliceCoord')&&length(Calib.SliceCoord)>=Z
250    Zindex=Z;
251    Zphys=Calib.SliceCoord(Zindex,3);%GENERALISER AUX CAS AVEC ANGLE
252else
253    Zphys=0;
254end
255if ~exist('X','var')||~exist('Y','var')
256    Xphys=[];
257    Yphys=[];%default
258    return
259end
260%coordinate transform
261if ~isfield(Calib,'fx_fy')
262     Calib.fx_fy=[1 1];
263end
264if ~isfield(Calib,'Tx_Ty_Tz')
265     Calib.Tx_Ty_Tz=[0 0 1];
266end
267if ~isfield(Calib,'Cx_Cy')
268     Calib.Cx_Cy=[0 0];
269end
270if ~isfield(Calib,'kc')
271     Calib.kc=0;
272end
273if isfield(Calib,'R')
274    R=(Calib.R)';
275    Tx=Calib.Tx_Ty_Tz(1);
276    Ty=Calib.Tx_Ty_Tz(2);
277    Tz=Calib.Tx_Ty_Tz(3);
278    f=Calib.fx_fy(1);%dpy=1; sx=1
279    dpx=Calib.fx_fy(2)/Calib.fx_fy(1);
280    Dx=R(5)*R(7)-R(4)*R(8);
281    Dy=R(1)*R(8)-R(2)*R(7);
282    D0=f*(R(2)*R(4)-R(1)*R(5));
283    Z11=R(6)*R(8)-R(5)*R(9);
284    Z12=R(2)*R(9)-R(3)*R(8); 
285    Z21=R(4)*R(9)-R(6)*R(7);
286    Z22=R(3)*R(7)-R(1)*R(9);
287    Zx0=R(3)*R(5)-R(2)*R(6);
288    Zy0=R(1)*R(6)-R(3)*R(4);
289    A11=R(8)*Ty-R(5)*Tz+Z11*Zphys;
290    A12=R(2)*Tz-R(8)*Tx+Z12*Zphys;
291    A21=-R(7)*Ty+R(4)*Tz+Z21*Zphys;
292    A22=-R(1)*Tz+R(7)*Tx+Z22*Zphys;
293    X0=f*(R(5)*Tx-R(2)*Ty+Zx0*Zphys);
294    Y0=f*(-R(4)*Tx+R(1)*Ty+Zy0*Zphys);
295        %px to camera:
296    Xd=dpx*(X-Calib.Cx_Cy(1)); % sensor coordinates
297    Yd=(Y-Calib.Cx_Cy(2));
298    dist_fact=1+Calib.kc*(Xd.*Xd+Yd.*Yd)/(f*f); %distortion factor
299    Xu=Xd./dist_fact;%undistorted sensor coordinates
300    Yu=Yd./dist_fact;
301    denom=Dx*Xu+Dy*Yu+D0;
302    % denom2=denom.*denom;
303    Xphys=(A11.*Xu+A12.*Yu+X0)./denom;%world coordinates
304    Yphys=(A21.*Xu+A22.*Yu+Y0)./denom;
305%     Xd=(X-Calib.Cx_Cy(1))/Calib.fx_fy(1); % sensor coordinates
306%     Yd=(Y-Calib.Cx_Cy(2))/Calib.fx_fy(2);
307%     dist_fact=1+Calib.kc*(Xd.*Xd+Yd.*Yd); %distortion factor
308%     Xu=Xd./dist_fact;%undistorted sensor coordinates
309%     Yu=Yd./dist_fact;
310%     A11=R(7)*Xu-R(1);
311%     A12=R(8)*Xu-R(2);
312%     A21=R(7)*Yu-R(4);
313%     A22=R(8)*Yu-R(5);
314%     B1=(R(3)-R(9)*Xu)*Zphys-Tz*Xu+Tx;
315%     B2=(R(6)-R(9)*Yu)*Zphys-Tz*Yu+Ty;
316%     deter=A12.*A21-A11.*A22;
317%     Xphys=(A21.*B1-A11.*B2)./deter;
318%     Yphys=(-A22.*B1+A12.*B2)./deter;
319else
320    Xphys=-Calib.Tx_Ty_Tz(1)+X/Calib.fx_fy(1);
321    Yphys=-Calib.Tx_Ty_Tz(2)+Y/Calib.fx_fy(2);
322end
323
324%'px_XYZ': transform phys coordinates to image coordinates (px)
325%
326% OUPUT:
327% X,Y: array of coordinates in the image cooresponding to the input physical positions
328%                    (origin at lower leftcorner, unit=pixel)
329
330% INPUT:
331% Calib: structure containing the calibration parameters (read from the ImaDoc .xml file)
332% Xphys, Yphys: array of x,y physical coordinates
333% [Zphys]: corresponding array of z physical coordinates (0 by default)
334
335
336
337
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