 Timestamp:
 Dec 6, 2014, 4:42:43 PM (10 years ago)
 File:

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trunk/src/transform_field/phys.m
r810 r836 144 144 %% transform the scalar(s) or image(s) 145 145 if iscalar~=0 146 [A,Coord_x,Coord_y]=phys_ Ima(A,Calib,ZIndex);%TODO : introduire interp2_uvmat ds phys_ima146 [A,Coord_x,Coord_y]=phys_ima(A,XmlData,ZIndex);%TODO : introduire interp2_uvmat ds phys_ima 147 147 if iscalar==1 && ~isempty(DataOut_1) % case for which only the second field is a scalar 148 148 DataOut_1.A=A{1}; … … 238 238 239 239 %%%%%%%%%%%%%%%%%%%% 240 function [A_out,Rangx,Rangy]=phys_Ima(A,CalibIn,ZIndex) 241 xcorner=[]; 242 ycorner=[]; 243 npx=[]; 244 npy=[]; 245 dx=ones(1,numel(A)); 246 dy=ones(1,numel(A)); 247 for icell=1:numel(A) 248 siz=size(A{icell}); 249 npx=[npx siz(2)]; 250 npy=[npy siz(1)]; 251 Calib=CalibIn{icell}; 252 xima=[0.5 siz(2)0.5 0.5 siz(2)0.5];%image coordinates of corners 253 yima=[0.5 0.5 siz(1)0.5 siz(1)0.5]; 254 [xcorner_new,ycorner_new]=phys_XYZ(Calib,xima,yima,ZIndex);%corresponding physical coordinates 255 dx(icell)=(max(xcorner_new)min(xcorner_new))/(siz(2)1); 256 dy(icell)=(max(ycorner_new)min(ycorner_new))/(siz(1)1); 257 xcorner=[xcorner xcorner_new]; 258 ycorner=[ycorner ycorner_new]; 259 end 260 Rangx(1)=min(xcorner); 261 Rangx(2)=max(xcorner); 262 Rangy(2)=min(ycorner); 263 Rangy(1)=max(ycorner); 264 test_multi=(max(npx)~=min(npx))  (max(npy)~=min(npy)); %different image lengths 265 npX=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) 266 npY=1+round((Rangy(1)Rangy(2))/min(dy)); 267 x=linspace(Rangx(1),Rangx(2),npX); 268 y=linspace(Rangy(1),Rangy(2),npY); 269 [X,Y]=meshgrid(x,y);%grid in physical coordiantes 270 %vec_B=[]; 271 A_out=cell(1,numel(A)); 272 for icell=1:length(A) 273 Calib=CalibIn{icell}; 274 % rescaling of the image coordinates without change of the image array 275 if strcmp(Calib.CalibrationType,'rescale') && isequal(Calib,CalibIn{1}) 276 A_out{icell}=A{icell};%no transform 277 Rangx=[0.5 npx0.5];%image coordiantes of corners 278 Rangy=[npy0.5 0.5]; 279 [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation 280 [xx,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,ZIndex); 281 else 282 % the image needs to be interpolated to the new coordinates 283 zphys=0; %default 284 if isfield(Calib,'SliceCoord') %.Z= index of plane 285 SliceCoord=Calib.SliceCoord(ZIndex,:); 286 zphys=SliceCoord(3); %to generalize for nonparallel planes 287 if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex') 288 H=Calib.InterfaceCoord(3); 289 if H>zphys 290 zphys=H(Hzphys)/Calib.RefractionIndex; %corrected z (virtual object) 291 end 292 end 293 end 294 xima=0.5:npx0.5;%image coordinates of corners 295 yima=npy0.5:1:0.5; 296 [XIMA_init,YIMA_init]=meshgrid(xima,yima);%grid of initial image in px coordinates 297 [XIMA,YIMA]=px_XYZ(CalibIn{icell},X,Y,zphys);% image coordinates for each point in the real 298 %[XPHYS_init,YPHYS_init]=phys_XYZ(Calib,XIMA_init,YIMA_init,ZIndex); 299 testuint8=isa(A{icell},'uint8'); 300 testuint16=isa(A{icell},'uint16'); 301 if ndims(A{icell})==2 %(B/W images) 302 A_out{icell}=interp2(XIMA_init,YIMA_init,double(A{icell}),XIMA,YIMA); 303 % [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation 304 % [XIMA_init,YIMA_init]=px_XYZ(CalibIn{icell},X,Y,zphys);% image coordinates for each point in the real space grid 305 % 306 % XIMA=reshape(round(XIMA),1,npX*npY);%indices reorganized in 'line' 307 % YIMA=reshape(round(YIMA),1,npX*npY); 308 % flagin=XIMA>=1 & XIMA<=npx(icell) & YIMA >=1 & YIMA<=npy(icell);%flagin=1 inside the original image 309 310 % if numel(siz)==2 %(B/W images) 311 % vec_A=reshape(A{icell},1,npx(icell)*npy(icell));%put the original image in line 312 % %ind_in=find(flagin); 313 % ind_out=find(~flagin); 314 % ICOMB=((XIMA1)*npy(icell)+(npy(icell)+1YIMA)); 315 % ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A 316 % %vec_B(ind_in)=vec_A(ICOMB); 317 % vec_B(flagin)=vec_A(ICOMB); 318 % vec_B(~flagin)=zeros(size(ind_out)); 319 % % vec_B(ind_out)=zeros(size(ind_out)); 320 % A_out{icell}=reshape(vec_B,npY,npX);%new image in real coordinates 321 elseif ndims(A{icell})==3 322 for icolor=1:size(A{icell},3) 323 A{icell}=double(A{icell}); 324 A_out{icell}(:,:,icolor)=interp2(XIMA_init,YIMA_init,A{icell}(:,:,icolor),XIMA,YIMA); 325 % vec_A=reshape(A{icell}(:,:,icolor),1,npx*npy);%put the original image in line 326 % % ind_in=find(flagin); 327 % ind_out=find(~flagin); 328 % ICOMB=((XIMA1)*npy+(npy+1YIMA)); 329 % ICOMB=ICOMB(flagin);%index corresponding to XIMA and YIMA in the aligned original image vec_A 330 % vec_B(flagin)=vec_A(ICOMB); 331 % vec_B(~flagin)=zeros(size(ind_out)); 332 % A_out{icell}(:,:,icolor)=reshape(vec_B,npy,npx);%new image in real coordinates 333 end 334 end 335 if testuint8 336 A_out{icell}=uint8(A_out{icell}); 337 end 338 if testuint16 339 A_out{icell}=uint16(A_out{icell}); 340 end 341 end 342 end 343 240
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