source: trunk/src/transform_field/phys_polar.m @ 40

Last change on this file since 40 was 40, checked in by sommeria, 11 years ago

-relabel_i_j added to the svn (relabel an image series with two indices)
-Menu projection Object added to uvmat, rationalizes the call of projection objects (to improve yet)
-get_plot_handles: modified in relationwith the Menu projection object
-mouse_down: corrected in relation with previous change in field transforms
-transform_field functions added to the svn
-set_object and keyboard_callback: cleaning

File size: 12.3 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
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;
67if  ~isempty(Calib{1})
68    DataOut=phys_1(Data,Calib{1},origin_xy,radius_offset,angle_offset,angle_scale);
69    %case of images or scalar
70    if isfield(Data,'A')&isfield(Data,'AX')&~isempty(Data.AX) & isfield(Data,'AY')&...
71                                           ~isempty(Data.AY)&length(Data.A)>1
72        iscalar=1;
73        A{1}=Data.A;
74    end
75    %transform of X,Y coordinates for vector fields
76    if isfield(Data,'ZIndex')&~isempty(Data.ZIndex)
77        ZIndex=Data.ZIndex;
78    else
79        ZIndex=0;
80    end
81end
82
83if test_1
84    DataOut_1=phys_1(Data_1,Calib{2},origin_xy,radius_offset,angle_offset,angle_scale);
85    if isfield(Data_1,'A')&isfield(Data_1,'AX')&~isempty(Data_1.AX) & isfield(Data_1,'AY')&...
86                                       ~isempty(Data_1.AY)&length(Data_1.A)>1
87          iscalar=iscalar+1;
88          Calib{iscalar}=Calib{2};
89          A{iscalar}=Data_1.A;
90          if isfield(Data_1,'ZIndex')&~isequal(Data_1.ZIndex,ZIndex)
91              DataOut.Txt='inconsistent plane indexes in the two input fields';
92          end
93          if iscalar==1% case for which only the second field is a scalar
94               [A,AX,AY]=phys_Ima(A,Calib,ZIndex,origin_xy,radius_offset,angle_offset,angle_scale);
95               DataOut_1.A=A{1};
96               DataOut_1.AX=AX;
97               DataOut_1.AY=AY;
98               return
99          end
100    end
101end
102if iscalar~=0
103    [A,AX,AY]=phys_Ima(A,Calib,ZIndex,origin_xy,radius_offset,angle_offset,angle_scale);%
104    DataOut.A=A{1};
105    DataOut.AX=AX;
106    DataOut.AY=AY;
107    if iscalar==2
108        DataOut_1.A=A{2};
109        DataOut_1.AX=AX;
110        DataOut_1.AY=AY;
111    end
112end
113
114%------------------------------------------------
115function DataOut=phys_1(Data,Calib,origin_xy,radius_offset,angle_offset,angle_scale)
116
117DataOut=Data;
118DataOut.CoordType='phys'; %put flag for physical coordinates
119if isfield(Calib,'CoordUnit')
120    DataOut.CoordUnit=Calib.CoordUnit;
121else
122    DataOut.CoordUnit='cm'; %default
123end
124DataOut.TimeUnit='s';
125%perform a geometry transform if Calib contains a field .GeometryCalib
126if isfield(Data,'CoordType') && isequal(Data.CoordType,'px') && ~isempty(Calib)
127    if isfield(Data,'CoordUnit')
128         DataOut=rmfield(DataOut,'CoordUnit');
129    end
130    %transform of X,Y coordinates for vector fields
131    if isfield(Data,'ZIndex')&~isempty(Data.ZIndex)
132        Z=Data.ZIndex;
133    else
134        Z=0;
135    end
136    if isfield(Data,'X') &isfield(Data,'Y')&~isempty(Data.X) & ~isempty(Data.Y)
137        [DataOut.X,DataOut.Y,DataOut.Z]=phys_XYZ(Calib,Data.X,Data.Y,Z); %transform from pixels to physical
138        DataOut.X=DataOut.X-origin_xy(1);%origin of coordinates at the tank center
139        DataOut.Y=DataOut.Y-origin_xy(2);%origin of coordinates at the tank center
140        [theta,DataOut.X] = cart2pol(DataOut.X,DataOut.Y);%theta  and X are the polar coordinates angle and radius
141          %shift and renormalize the polar coordinates
142        DataOut.X=DataOut.X-radius_offset;%
143        DataOut.Y=theta*angle_scale-angle_offset;% normalized angle: distance along reference radius
144        %transform velocity field if exists
145        if isfield(Data,'U')&isfield(Data,'V')&~isempty(Data.U) & ~isempty(Data.V)& isfield(Data,'dt')
146            if ~isempty(Data.dt)
147            [XOut_1,YOut_1]=phys_XYZ(Calib,Data.X-Data.U/2,Data.Y-Data.V/2,Z);
148            [XOut_2,YOut_2]=phys_XYZ(Calib,Data.X+Data.U/2,Data.Y+Data.V/2,Z);
149            UX=(XOut_2-XOut_1)/Data.dt;
150            VY=(YOut_2-YOut_1)/Data.dt;     
151            %transform u,v into polar coordiantes
152            DataOut.U=UX.*cos(theta)+VY.*sin(theta);%radial velocity
153            DataOut.V=(-UX.*sin(theta)+VY.*cos(theta));%./(DataOut.X)%+radius_ref);%angular velocity calculated
154            %shift and renormalize the angular velocity
155            end
156        end
157    end
158end
159
160 
161%%%%%%%%%%%%%%%%%%%%
162function [A_out,Rangx,Rangy]=phys_Ima(A,CalibIn,ZIndex,origin_xy,radius_offset,angle_offset,angle_scale)
163xcorner=[];
164ycorner=[];
165npx=[];
166npy=[];
167
168for icell=1:length(A)
169    siz=size(A{icell});
170    npx=[npx siz(2)];
171    npy=[npy siz(1)];
172    zphys=0; %default
173    if isfield(CalibIn{icell},'SliceCoord') %.Z= index of plane
174       SliceCoord=CalibIn{icell}.SliceCoord(ZIndex,:);
175       zphys=SliceCoord(3); %to generalize for non-parallel planes
176    end
177    xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordiantes of corners
178    yima=[0.5 0.5 siz(1)-0.5 siz(1)-0.5];
179    [xcorner_new,ycorner_new]=phys_XYZ(CalibIn{icell},xima,yima,ZIndex);%corresponding physical coordinates
180    %transform the corner coordinates into polar ones   
181    xcorner_new=xcorner_new-origin_xy(1);%shift to the origin of the polar coordinates
182    ycorner_new=ycorner_new-origin_xy(2);%shift to the origin of the polar coordinates       
183    [theta,xcorner_new] = cart2pol(xcorner_new,ycorner_new);%theta  and X are the polar coordinates angle and radius
184    if (max(theta)-min(theta))>pi   %if the polar origin is inside the image
185        xcorner_new=[0 max(xcorner_new)];
186        theta=[-pi pi];
187    end
188          %shift and renormalize the polar coordinates
189    xcorner_new=xcorner_new-radius_offset;%
190    ycorner_new=theta*angle_scale-angle_offset;% normalized angle: distance along reference radius
191    xcorner=[xcorner xcorner_new];
192    ycorner=[ycorner ycorner_new];
193end
194Rangx(1)=min(xcorner);
195Rangx(2)=max(xcorner);
196Rangy(2)=min(ycorner);
197Rangy(1)=max(ycorner);
198% test_multi=(max(npx)~=min(npx)) | (max(npy)~=min(npy));
199npx=max(npx);
200npy=max(npy);
201x=linspace(Rangx(1),Rangx(2),npx);
202y=linspace(Rangy(1),Rangy(2),npy);
203[X,Y]=meshgrid(x,y);%grid in physical coordinates
204%transform X, Y in cartesian
205X=X+radius_offset;%
206Y=(Y+angle_offset)/angle_scale;% normalized angle: distance along reference radius
207[X,Y] = pol2cart(Y,X);
208X=X+origin_xy(1);%shift to the origin of the polar coordinates
209Y=Y+origin_xy(2);%shift to the origin of the polar coordinates
210for icell=1:length(A)
211    [XIMA,YIMA]=px_XYZ(CalibIn{icell},X,Y,zphys);%corresponding image indices for each point in the real space grid
212    XIMA=reshape(round(XIMA),1,npx*npy);%indices reorganized in 'line'
213    YIMA=reshape(round(YIMA),1,npx*npy);
214    flagin=XIMA>=1 & XIMA<=npx & YIMA >=1 & YIMA<=npy;%flagin=1 inside the original image
215    vec_A=reshape(A{icell}(:,:,1),1,npx*npy);%put the original image in line
216    ind_in=find(flagin);
217    ind_out=find(~flagin);
218    ICOMB=((XIMA-1)*npy+(npy+1-YIMA));
219    ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A
220    vec_B(ind_in)=vec_A(ICOMB);
221    vec_B(ind_out)=zeros(size(ind_out));
222    A_out{icell}=reshape(vec_B,npy,npx);%new image in real coordinates
223end
224%Rangx=Rangx-radius_offset;
225
226%'phys_XYZ':transforms image (px) to real world (phys) coordinates using geometric calibration parameters
227% function [Xphys,Yphys]=phys_XYZ(Calib,X,Y,Z)
228%
229%OUTPUT:
230%
231%INPUT:
232%Z: index of plane
233function [Xphys,Yphys,Zphys]=phys_XYZ(Calib,X,Y,Z)
234if exist('Z','var')& isequal(Z,round(Z))& Z>0 & isfield(Calib,'SliceCoord')&length(Calib.SliceCoord)>=Z
235    Zindex=Z;
236    Zphys=Calib.SliceCoord(Zindex,3);%GENERALISER AUX CAS AVEC ANGLE
237else
238%     if exist('Z','var')
239%         Zphys=Z;
240%     else
241        Zphys=0;
242%     end
243end
244if ~exist('X','var')||~exist('Y','var')
245    Xphys=[];
246    Yphys=[];%default
247    return
248end
249Xphys=X;%default
250Yphys=Y;
251%image transform
252if isfield(Calib,'R')
253    R=(Calib.R)';
254    Dx=R(5)*R(7)-R(4)*R(8);
255    Dy=R(1)*R(8)-R(2)*R(7);
256    D0=Calib.f*(R(2)*R(4)-R(1)*R(5));
257    Z11=R(6)*R(8)-R(5)*R(9);
258    Z12=R(2)*R(9)-R(3)*R(8); 
259    Z21=R(4)*R(9)-R(6)*R(7);
260    Z22=R(3)*R(7)-R(1)*R(9);
261    Zx0=R(3)*R(5)-R(2)*R(6);
262    Zy0=R(1)*R(6)-R(3)*R(4);
263    A11=R(8)*Calib.Ty-R(5)*Calib.Tz+Z11*Zphys;
264    A12=R(2)*Calib.Tz-R(8)*Calib.Tx+Z12*Zphys;
265    A21=-R(7)*Calib.Ty+R(4)*Calib.Tz+Z21*Zphys;
266    A22=-R(1)*Calib.Tz+R(7)*Calib.Tx+Z11*Zphys;
267    X0=Calib.f*(R(5)*Calib.Tx-R(2)*Calib.Ty+Zx0*Zphys);
268    Y0=Calib.f*(-R(4)*Calib.Tx+R(1)*Calib.Ty+Zy0*Zphys);
269        %px to camera:
270    Xd=(Calib.dpx/Calib.sx)*(X-Calib.Cx); % sensor coordinates
271    Yd=Calib.dpy*(Y-Calib.Cy);
272    dist_fact=1+Calib.kappa1*(Xd.*Xd+Yd.*Yd); %distortion factor
273    Xu=dist_fact.*Xd;%undistorted sensor coordinates
274    Yu=dist_fact.*Yd;
275    denom=Dx*Xu+Dy*Yu+D0;
276    % denom2=denom.*denom;
277    Xphys=(A11.*Xu+A12.*Yu+X0)./denom;%world coordinates
278    Yphys=(A21.*Xu+A22.*Yu+Y0)./denom;
279end
280
281%'px_XYZ': transform phys coordinates to image coordinates (px)
282%
283% OUPUT:
284% X,Y: array of coordinates in the image cooresponding to the input physical positions
285%                    (origin at lower leftcorner, unit=pixel)
286
287% INPUT:
288% Calib: structure containing the calibration parameters (read from the ImaDoc .xml file)
289% Xphys, Yphys: array of x,y physical coordinates
290% [Zphys]: corresponding array of z physical coordinates (0 by default)
291
292
293function [X,Y]=px_XYZ(Calib,Xphys,Yphys,Zphys)
294X=[];%default
295Y=[];
296% if exist('Z','var')& isequal(Z,round(Z))& Z>0 & isfield(Calib,'PlanePos')&length(Calib.PlanePos)>=Z
297%     Zindex=Z;
298%     planepos=Calib.PlanePos{Zindex};
299%     zphys=planepos(3);%A GENERALISER CAS AVEC ANGLE
300% else
301%     zphys=0;
302% end
303if ~exist('Zphys','var')
304    Zphys=0;
305end
306
307%%%%%%%%%%%%%
308if isfield(Calib,'R')
309    R=(Calib.R)';
310    xc=R(1)*Xphys+R(2)*Yphys+R(3)*Zphys+Calib.Tx;
311    yc=R(4)*Xphys+R(5)*Yphys+R(6)*Zphys+Calib.Ty;
312    zc=R(7)*Xphys+R(8)*Yphys+R(9)*Zphys+Calib.Tz;
313%undistorted image coordinates
314    Xu=Calib.f*xc./zc;
315    Yu=Calib.f*yc./zc;
316%distorted image coordinates
317    distortion=(Calib.kappa1)*(Xu.*Xu+Yu.*Yu)+1; %A REVOIR
318% distortion=1;
319    Xd=Xu./distortion;
320    Yd=Yu./distortion;
321%pixel coordinates
322    X=Xd*Calib.sx/Calib.dpx+Calib.Cx;
323    Y=Yd/Calib.dpy+Calib.Cy;
324
325elseif isfield(Calib,'Pxcmx')&isfield(Calib,'Pxcmy')%old calib 
326        X=Xphys*Calib.Pxcmx;
327        Y=Yphys*Calib.Pxcmy;
328end
329
330
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