source: trunk/src/transform_field/phys_polar.m @ 118

Last change on this file since 118 was 93, checked in by sommeria, 14 years ago

FFT: improved to deal with NaN data
merge_proj: corrected to reproduce dt if unique
uvmat.fig: tooltip corrected
plot_field: bug for isocontour corrected,
im_filter: cleaning
phys_polar: spatial derivative included (still to check)
set_obeject.fig: minor correction
struct2nc: comments improved
uvmat: button NB implemented
read_civxdata: error message improved

File size: 13.6 KB
Line 
1%transform image coordinates (px) to physical coordinates
2% then transform to polar coordinates:
3%[DataOut,DataOut_1]=phys_polar(varargin)
4%
5% OUTPUT:
6% DataOut: structure of modified data field: .X=radius, .Y=azimuth angle, .U, .V are radial and azimuthal velocity components
7% DataOut_1:  second data field (if two fields are in input)
8%
9%INPUT:
10% Data:  structure of input data (like UvData)
11% CalibData= structure containing the field .GeometryCalib with calibration parameters
12% Data_1:  second input field (not mandatory)
13% CalibData_1= calibration parameters for the second field
14
15function [DataOut,DataOut_1]=phys_polar(varargin)
16Calib{1}=[];
17if nargin==2||nargin==4
18    Data=varargin{1};
19    DataOut=Data;%default
20    DataOut_1=[];%default
21    CalibData=varargin{2};
22    if isfield(CalibData,'GeometryCalib')
23        Calib{1}=CalibData.GeometryCalib;
24    end
25    Calib{2}=Calib{1};
26else
27    DataOut.Txt='wrong input: need two or four structures';
28end
29test_1=0;
30if nargin==4% case of two input fields
31    test_1=1;
32    Data_1=varargin{3};
33    DataOut_1=Data_1;%default
34    CalibData_1=varargin{4};
35    if isfield(CalibData_1,'GeometryCalib')
36        Calib{2}=CalibData_1.GeometryCalib;
37    end
38end
39
40%parameters for polar coordinates (taken from the calibration data of the first field)
41%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
42origin_xy=[0 0];%center for the polar coordinates in the original x,y coordinates
43if isfield(Calib{1},'PolarCentre') && isnumeric(Calib{1}.PolarCentre)
44    if isequal(length(Calib{1}.PolarCentre),2);
45        origin_xy= Calib{1}.PolarCentre;
46    end
47end
48radius_offset=0;%reference radius used to offset the radial coordinate r
49angle_offset=0; %reference angle used as new origin of the polar angle (= axis Ox by default)
50if isfield(Calib{1},'PolarReferenceRadius') && isnumeric(Calib{1}.PolarReferenceRadius)
51    radius_offset=Calib{1}.PolarReferenceRadius;
52end
53if radius_offset > 0
54    angle_scale=radius_offset; %the azimuth is rescale in terms of the length along the reference radius
55else
56    angle_scale=180/pi; %polar angle in degrees
57end
58if isfield(Calib{1},'PolarReferenceAngle') && isnumeric(Calib{1}.PolarReferenceAngle)
59    angle_offset=Calib{1}.PolarReferenceAngle; %offset angle (in unit of the final angle, degrees or arc length along the reference radius))
60end
61% new x coordinate = radius-radius_offset;
62% new y coordinate = theta*angle_scale-angle_offset
63
64%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
65
66iscalar=0;
67%transform first field to cartesian phys coordiantes
68if  ~isempty(Calib{1})
69    DataOut=phys_1(Data,Calib{1},origin_xy,radius_offset,angle_offset,angle_scale);
70    %case of images or scalar
71    if isfield(Data,'A')&isfield(Data,'AX')&~isempty(Data.AX) & isfield(Data,'AY')&...
72                                           ~isempty(Data.AY)&length(Data.A)>1
73        iscalar=1;
74        A{1}=Data.A;
75    end
76    %transform of X,Y coordinates for vector fields
77    if isfield(Data,'ZIndex')&~isempty(Data.ZIndex)
78        ZIndex=Data.ZIndex;
79    else
80        ZIndex=0;
81    end
82end
83%transform second field (if exists) to cartesian phys coordiantes
84if test_1
85    DataOut_1=phys_1(Data_1,Calib{2},origin_xy,radius_offset,angle_offset,angle_scale);
86    if isfield(Data_1,'A')&isfield(Data_1,'AX')&~isempty(Data_1.AX) & isfield(Data_1,'AY')&...
87                                       ~isempty(Data_1.AY)&length(Data_1.A)>1
88          iscalar=iscalar+1;
89          Calib{iscalar}=Calib{2};
90          A{iscalar}=Data_1.A;
91          if isfield(Data_1,'ZIndex')&~isequal(Data_1.ZIndex,ZIndex)
92              DataOut.Txt='inconsistent plane indexes in the two input fields';
93          end
94          if iscalar==1% case for which only the second field is a scalar
95               [A,AX,AY]=phys_Ima(A,Calib,ZIndex,origin_xy,radius_offset,angle_offset,angle_scale);
96               DataOut_1.A=A{1};
97               DataOut_1.AX=AX;
98               DataOut_1.AY=AY;
99               return
100          end
101    end
102end
103if iscalar~=0
104    [A,AX,AY]=phys_Ima(A,Calib,ZIndex,origin_xy,radius_offset,angle_offset,angle_scale);%
105    DataOut.A=A{1};
106    DataOut.AX=AX;
107    DataOut.AY=AY;
108    if iscalar==2
109        DataOut_1.A=A{2};
110        DataOut_1.AX=AX;
111        DataOut_1.AY=AY;
112    end
113end
114
115%------------------------------------------------
116function DataOut=phys_1(Data,Calib,origin_xy,radius_offset,angle_offset,angle_scale)
117
118DataOut=Data;
119DataOut.CoordType='phys'; %put flag for physical coordinates
120if isfield(Calib,'CoordUnit')
121    DataOut.CoordUnit=Calib.CoordUnit;
122else
123    DataOut.CoordUnit='cm'; %default
124end
125DataOut.TimeUnit='s';
126%perform a geometry transform if Calib contains a field .GeometryCalib
127if isfield(Data,'CoordType') && isequal(Data.CoordType,'px') && ~isempty(Calib)
128    if isfield(Data,'CoordUnit')
129         DataOut=rmfield(DataOut,'CoordUnit');
130    end
131    %transform of X,Y coordinates for vector fields
132    if isfield(Data,'ZIndex')&~isempty(Data.ZIndex)
133        Z=Data.ZIndex;
134    else
135        Z=0;
136    end
137    if isfield(Data,'X') &isfield(Data,'Y')&~isempty(Data.X) & ~isempty(Data.Y)
138        [DataOut.X,DataOut.Y,DataOut.Z]=phys_XYZ(Calib,Data.X,Data.Y,Z); %transform from pixels to physical
139        DataOut.X=DataOut.X-origin_xy(1);%origin of coordinates at the tank center
140        DataOut.Y=DataOut.Y-origin_xy(2);%origin of coordinates at the tank center
141        [theta,DataOut.X] = cart2pol(DataOut.X,DataOut.Y);%theta  and X are the polar coordinates angle and radius
142          %shift and renormalize the polar coordinates
143        DataOut.X=DataOut.X-radius_offset;%
144        DataOut.Y=theta*angle_scale-angle_offset;% normalized angle: distance along reference radius
145        %transform velocity field if exists
146        if isfield(Data,'U')&isfield(Data,'V')&~isempty(Data.U) & ~isempty(Data.V)& isfield(Data,'dt')
147            if ~isempty(Data.dt)
148            [XOut_1,YOut_1]=phys_XYZ(Calib,Data.X-Data.U/2,Data.Y-Data.V/2,Z);
149            [XOut_2,YOut_2]=phys_XYZ(Calib,Data.X+Data.U/2,Data.Y+Data.V/2,Z);
150            UX=(XOut_2-XOut_1)/Data.dt;
151            VY=(YOut_2-YOut_1)/Data.dt;     
152            %transform u,v into polar coordiantes
153            DataOut.U=UX.*cos(theta)+VY.*sin(theta);%radial velocity
154            DataOut.V=(-UX.*sin(theta)+VY.*cos(theta));%./(DataOut.X)%+radius_ref);%angular velocity calculated
155            %shift and renormalize the angular velocity
156            end
157        end
158        %transform of spatial derivatives
159        if isfield(Data,'X') && ~isempty(Data.X) && isfield(Data,'DjUi') && ~isempty(Data.DjUi)...
160                && isfield(Data,'dt')
161            if ~isempty(Data.dt)
162                % estimate the Jacobian matrix DXpx/DXphys
163                for ip=1:length(Data.X)
164                    [Xp1,Yp1]=phys_XYZ(Calib,Data.X(ip)+0.5,Data.Y(ip),Z);
165                    [Xm1,Ym1]=phys_XYZ(Calib,Data.X(ip)-0.5,Data.Y(ip),Z);
166                    [Xp2,Yp2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)+0.5,Z);
167                    [Xm2,Ym2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)-0.5,Z);
168                    %Jacobian matrix DXpphys/DXpx
169                    DjXi(1,1)=(Xp1-Xm1);
170                    DjXi(2,1)=(Yp1-Ym1);
171                    DjXi(1,2)=(Xp2-Xm2);
172                    DjXi(2,2)=(Yp2-Ym2);
173                    DjUi(:,:)=Data.DjUi(ip,:,:);
174                    DjUi=(DjXi*DjUi')/DjXi;% =J-1*M*J , curvature effects (derivatives of J) neglected
175                    DataOut.DjUi(ip,:,:)=DjUi';
176                end
177                DataOut.DjUi =  DataOut.DjUi/Data.dt;   %     min(Data.DjUi(:,1,1))=DUDX
178            end
179        end
180    end
181end
182
183 
184%%%%%%%%%%%%%%%%%%%%
185function [A_out,Rangx,Rangy]=phys_Ima(A,CalibIn,ZIndex,origin_xy,radius_offset,angle_offset,angle_scale)
186xcorner=[];
187ycorner=[];
188npx=[];
189npy=[];
190
191for icell=1:length(A)
192    siz=size(A{icell});
193    npx=[npx siz(2)];
194    npy=[npy siz(1)];
195    zphys=0; %default
196    if isfield(CalibIn{icell},'SliceCoord') %.Z= index of plane
197       SliceCoord=CalibIn{icell}.SliceCoord(ZIndex,:);
198       zphys=SliceCoord(3); %to generalize for non-parallel planes
199    end
200    xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordiantes of corners
201    yima=[0.5 0.5 siz(1)-0.5 siz(1)-0.5];
202    [xcorner_new,ycorner_new]=phys_XYZ(CalibIn{icell},xima,yima,ZIndex);%corresponding physical coordinates
203    %transform the corner coordinates into polar ones   
204    xcorner_new=xcorner_new-origin_xy(1);%shift to the origin of the polar coordinates
205    ycorner_new=ycorner_new-origin_xy(2);%shift to the origin of the polar coordinates       
206    [theta,xcorner_new] = cart2pol(xcorner_new,ycorner_new);%theta  and X are the polar coordinates angle and radius
207    if (max(theta)-min(theta))>pi   %if the polar origin is inside the image
208        xcorner_new=[0 max(xcorner_new)];
209        theta=[-pi pi];
210    end
211          %shift and renormalize the polar coordinates
212    xcorner_new=xcorner_new-radius_offset;%
213    ycorner_new=theta*angle_scale-angle_offset;% normalized angle: distance along reference radius
214    xcorner=[xcorner xcorner_new];
215    ycorner=[ycorner ycorner_new];
216end
217Rangx(1)=min(xcorner);
218Rangx(2)=max(xcorner);
219Rangy(2)=min(ycorner);
220Rangy(1)=max(ycorner);
221% test_multi=(max(npx)~=min(npx)) | (max(npy)~=min(npy));
222npx=max(npx);
223npy=max(npy);
224x=linspace(Rangx(1),Rangx(2),npx);
225y=linspace(Rangy(1),Rangy(2),npy);
226[X,Y]=meshgrid(x,y);%grid in physical coordinates
227%transform X, Y in cartesian
228X=X+radius_offset;%
229Y=(Y+angle_offset)/angle_scale;% normalized angle: distance along reference radius
230[X,Y] = pol2cart(Y,X);
231X=X+origin_xy(1);%shift to the origin of the polar coordinates
232Y=Y+origin_xy(2);%shift to the origin of the polar coordinates
233for icell=1:length(A)
234    [XIMA,YIMA]=px_XYZ(CalibIn{icell},X,Y,zphys);%corresponding image indices for each point in the real space grid
235    XIMA=reshape(round(XIMA),1,npx*npy);%indices reorganized in 'line'
236    YIMA=reshape(round(YIMA),1,npx*npy);
237    flagin=XIMA>=1 & XIMA<=npx & YIMA >=1 & YIMA<=npy;%flagin=1 inside the original image
238    vec_A=reshape(A{icell}(:,:,1),1,npx*npy);%put the original image in line
239    ind_in=find(flagin);
240    ind_out=find(~flagin);
241    ICOMB=((XIMA-1)*npy+(npy+1-YIMA));
242    ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
243    vec_B(ind_in)=vec_A(ICOMB);
244    vec_B(ind_out)=zeros(size(ind_out));
245    A_out{icell}=reshape(vec_B,npy,npx);%new image in real coordinates
246end
247%Rangx=Rangx-radius_offset;
248
249%'phys_XYZ':transforms image (px) to real world (phys) coordinates using geometric calibration parameters
250% function [Xphys,Yphys]=phys_XYZ(Calib,X,Y,Z)
251%
252%OUTPUT:
253%
254%INPUT:
255%Z: index of plane
256function [Xphys,Yphys,Zphys]=phys_XYZ(Calib,X,Y,Z)
257if exist('Z','var')& isequal(Z,round(Z))& Z>0 & isfield(Calib,'SliceCoord')&length(Calib.SliceCoord)>=Z
258    Zindex=Z;
259    Zphys=Calib.SliceCoord(Zindex,3);%GENERALISER AUX CAS AVEC ANGLE
260else
261%     if exist('Z','var')
262%         Zphys=Z;
263%     else
264        Zphys=0;
265%     end
266end
267if ~exist('X','var')||~exist('Y','var')
268    Xphys=[];
269    Yphys=[];%default
270    return
271end
272Xphys=X;%default
273Yphys=Y;
274%image transform
275if isfield(Calib,'R')
276    R=(Calib.R)';
277    Dx=R(5)*R(7)-R(4)*R(8);
278    Dy=R(1)*R(8)-R(2)*R(7);
279    D0=Calib.f*(R(2)*R(4)-R(1)*R(5));
280    Z11=R(6)*R(8)-R(5)*R(9);
281    Z12=R(2)*R(9)-R(3)*R(8); 
282    Z21=R(4)*R(9)-R(6)*R(7);
283    Z22=R(3)*R(7)-R(1)*R(9);
284    Zx0=R(3)*R(5)-R(2)*R(6);
285    Zy0=R(1)*R(6)-R(3)*R(4);
286    A11=R(8)*Calib.Ty-R(5)*Calib.Tz+Z11*Zphys;
287    A12=R(2)*Calib.Tz-R(8)*Calib.Tx+Z12*Zphys;
288    A21=-R(7)*Calib.Ty+R(4)*Calib.Tz+Z21*Zphys;
289    A22=-R(1)*Calib.Tz+R(7)*Calib.Tx+Z11*Zphys;
290    X0=Calib.f*(R(5)*Calib.Tx-R(2)*Calib.Ty+Zx0*Zphys);
291    Y0=Calib.f*(-R(4)*Calib.Tx+R(1)*Calib.Ty+Zy0*Zphys);
292        %px to camera:
293    Xd=(Calib.dpx/Calib.sx)*(X-Calib.Cx); % sensor coordinates
294    Yd=Calib.dpy*(Y-Calib.Cy);
295    dist_fact=1+Calib.kappa1*(Xd.*Xd+Yd.*Yd); %distortion factor
296    Xu=dist_fact.*Xd;%undistorted sensor coordinates
297    Yu=dist_fact.*Yd;
298    denom=Dx*Xu+Dy*Yu+D0;
299    % denom2=denom.*denom;
300    Xphys=(A11.*Xu+A12.*Yu+X0)./denom;%world coordinates
301    Yphys=(A21.*Xu+A22.*Yu+Y0)./denom;
302end
303
304%'px_XYZ': transform phys coordinates to image coordinates (px)
305%
306% OUPUT:
307% X,Y: array of coordinates in the image cooresponding to the input physical positions
308%                    (origin at lower leftcorner, unit=pixel)
309
310% INPUT:
311% Calib: structure containing the calibration parameters (read from the ImaDoc .xml file)
312% Xphys, Yphys: array of x,y physical coordinates
313% [Zphys]: corresponding array of z physical coordinates (0 by default)
314
315
316function [X,Y]=px_XYZ(Calib,Xphys,Yphys,Zphys)
317X=[];%default
318Y=[];
319% if exist('Z','var')& isequal(Z,round(Z))& Z>0 & isfield(Calib,'PlanePos')&length(Calib.PlanePos)>=Z
320%     Zindex=Z;
321%     planepos=Calib.PlanePos{Zindex};
322%     zphys=planepos(3);%A GENERALISER CAS AVEC ANGLE
323% else
324%     zphys=0;
325% end
326if ~exist('Zphys','var')
327    Zphys=0;
328end
329
330%%%%%%%%%%%%%
331if isfield(Calib,'R')
332    R=(Calib.R)';
333    xc=R(1)*Xphys+R(2)*Yphys+R(3)*Zphys+Calib.Tx;
334    yc=R(4)*Xphys+R(5)*Yphys+R(6)*Zphys+Calib.Ty;
335    zc=R(7)*Xphys+R(8)*Yphys+R(9)*Zphys+Calib.Tz;
336%undistorted image coordinates
337    Xu=Calib.f*xc./zc;
338    Yu=Calib.f*yc./zc;
339%distorted image coordinates
340    distortion=(Calib.kappa1)*(Xu.*Xu+Yu.*Yu)+1; %A REVOIR
341% distortion=1;
342    Xd=Xu./distortion;
343    Yd=Yu./distortion;
344%pixel coordinates
345    X=Xd*Calib.sx/Calib.dpx+Calib.Cx;
346    Y=Yd/Calib.dpy+Calib.Cy;
347
348elseif isfield(Calib,'Pxcmx')&isfield(Calib,'Pxcmy')%old calib 
349        X=Xphys*Calib.Pxcmx;
350        Y=Yphys*Calib.Pxcmy;
351end
352
353
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