[892] | 1 | |
---|
[849] | 2 | % phys_ima: transform several images in phys coordinates on a common pixel grid |
---|
| 3 | %------------------------------------------------------------------------ |
---|
| 4 | % OUTPUT: |
---|
| 5 | % A_out: cell array of oitput images corresponding to the transform of the input images |
---|
| 6 | % Rangx, Rangy; vectors with two elements defining the phys positions of first and last pixels in each direction |
---|
| 7 | % (the same for all the ouput images) |
---|
| 8 | % |
---|
| 9 | % INPUT: |
---|
| 10 | % A: cell array of input images |
---|
| 11 | % XmlData: cell array of structures defining the calibration parameters for each image |
---|
| 12 | % ZIndex: index of the reference plane used to define the phys position in 3D |
---|
| 13 | |
---|
| 14 | function [A_out,Rangx,Rangy]=phys_ima(A,XmlData,ZIndex) |
---|
| 15 | xcorner=[]; |
---|
| 16 | ycorner=[]; |
---|
| 17 | npx=[]; |
---|
| 18 | npy=[]; |
---|
| 19 | dx=ones(1,numel(A)); |
---|
| 20 | dy=ones(1,numel(A)); |
---|
| 21 | if isstruct(XmlData) |
---|
| 22 | XmlData={XmlData}; |
---|
| 23 | end |
---|
| 24 | for icell=1:numel(A) |
---|
| 25 | siz=size(A{icell}); |
---|
| 26 | npx=[npx siz(2)]; |
---|
| 27 | npy=[npy siz(1)]; |
---|
| 28 | Calib=XmlData{icell}.GeometryCalib; |
---|
| 29 | xima=[0.5 siz(2)-0.5 0.5 siz(2)-0.5];%image coordinates of corners |
---|
| 30 | yima=[0.5 0.5 siz(1)-0.5 siz(1)-0.5]; |
---|
| 31 | [xcorner_new,ycorner_new]=phys_XYZ(Calib,xima,yima,ZIndex);%corresponding physical coordinates |
---|
| 32 | dx(icell)=(max(xcorner_new)-min(xcorner_new))/(siz(2)-1); |
---|
| 33 | dy(icell)=(max(ycorner_new)-min(ycorner_new))/(siz(1)-1); |
---|
| 34 | xcorner=[xcorner xcorner_new]; |
---|
| 35 | ycorner=[ycorner ycorner_new]; |
---|
| 36 | end |
---|
| 37 | Rangx(1)=min(xcorner); |
---|
| 38 | Rangx(2)=max(xcorner); |
---|
| 39 | Rangy(2)=min(ycorner); |
---|
| 40 | Rangy(1)=max(ycorner); |
---|
| 41 | test_multi=(max(npx)~=min(npx)) || (max(npy)~=min(npy)); %different image lengths |
---|
[922] | 42 | % 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) |
---|
| 43 | % npY=1+round((Rangy(1)-Rangy(2))/min(dy)); |
---|
| 44 | |
---|
| 45 | npX=1+round((Rangx(2)-Rangx(1))/max(dx));% nbre of pixels in the new image (use the largest resolution max(dx) in the set of images) |
---|
| 46 | npY=1+round((Rangy(1)-Rangy(2))/max(dy)); |
---|
| 47 | |
---|
| 48 | |
---|
[849] | 49 | x=linspace(Rangx(1),Rangx(2),npX); |
---|
| 50 | y=linspace(Rangy(1),Rangy(2),npY); |
---|
| 51 | [X,Y]=meshgrid(x,y);%grid in physical coordiantes |
---|
| 52 | %vec_B=[]; |
---|
| 53 | A_out=cell(1,numel(A)); |
---|
| 54 | for icell=1:length(A) |
---|
| 55 | Calib=XmlData{icell}.GeometryCalib; |
---|
| 56 | % rescaling of the image coordinates without change of the image array |
---|
| 57 | if strcmp(Calib.CalibrationType,'rescale') && isequal(Calib,XmlData{1}.GeometryCalib) |
---|
| 58 | A_out{icell}=A{icell};%no transform |
---|
| 59 | Rangx=[0.5 npx-0.5];%image coordiantes of corners |
---|
| 60 | Rangy=[npy-0.5 0.5]; |
---|
| 61 | [Rangx]=phys_XYZ(Calib,Rangx,[0.5 0.5],ZIndex);%case of translations without rotation and quadratic deformation |
---|
| 62 | [xx,Rangy]=phys_XYZ(Calib,[0.5 0.5],Rangy,ZIndex); |
---|
| 63 | else |
---|
| 64 | % the image needs to be interpolated to the new coordinates |
---|
| 65 | zphys=0; %default |
---|
| 66 | if isfield(Calib,'SliceCoord') %.Z= index of plane |
---|
| 67 | SliceCoord=Calib.SliceCoord(ZIndex,:); |
---|
| 68 | zphys=SliceCoord(3); %to generalize for non-parallel planes |
---|
[892] | 69 | % if isfield(Calib,'InterfaceCoord') && isfield(Calib,'RefractionIndex') |
---|
| 70 | % H=Calib.InterfaceCoord(3); |
---|
| 71 | % if H>zphys |
---|
| 72 | % zphys=H-(H-zphys)/Calib.RefractionIndex; %corrected z (virtual object) |
---|
| 73 | % end |
---|
| 74 | % end |
---|
[849] | 75 | end |
---|
[922] | 76 | xima=0.5:npx(icell)-0.5;%image coordinates of corners |
---|
| 77 | yima=npy(icell)-0.5:-1:0.5; |
---|
[849] | 78 | [XIMA_init,YIMA_init]=meshgrid(xima,yima);%grid of initial image in px coordinates |
---|
| 79 | [XIMA,YIMA]=px_XYZ(XmlData{icell}.GeometryCalib,X,Y,zphys);% image coordinates for each point in the real |
---|
| 80 | testuint8=isa(A{icell},'uint8'); |
---|
| 81 | testuint16=isa(A{icell},'uint16'); |
---|
| 82 | if ndims(A{icell})==2 %(B/W images) |
---|
| 83 | A_out{icell}=interp2(XIMA_init,YIMA_init,double(A{icell}),XIMA,YIMA); |
---|
| 84 | elseif ndims(A{icell})==3 |
---|
| 85 | for icolor=1:size(A{icell},3) |
---|
| 86 | A{icell}=double(A{icell}); |
---|
| 87 | A_out{icell}(:,:,icolor)=interp2(XIMA_init,YIMA_init,A{icell}(:,:,icolor),XIMA,YIMA); |
---|
| 88 | end |
---|
| 89 | end |
---|
| 90 | if testuint8 |
---|
| 91 | A_out{icell}=uint8(A_out{icell}); |
---|
| 92 | end |
---|
| 93 | if testuint16 |
---|
| 94 | A_out{icell}=uint16(A_out{icell}); |
---|
| 95 | end |
---|
| 96 | end |
---|
| 97 | end |
---|