%'phys': transforms image (Unit='pixel') to real world (phys) coordinates using geometric calibration parameters. It acts if the input field contains the tag 'CoordTUnit' with value 'pixel' %------------------------------------------------------------------------ %%%% Use the general syntax for transform fields %%%% % OUTPUT: % DataOut: output field structure % %INPUT: % DataIn: first input field structure % XmlData: first input parameter structure, % .GeometryCalib: substructure of the calibration parameters % DataIn_1: optional second input field structure % XmlData_1: optional second input parameter structure % .GeometryCalib: substructure of the calibration parameters %======================================================================= % Copyright 2008-2014, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France % http://www.legi.grenoble-inp.fr % Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr % % This file is part of the toolbox UVMAT. % % UVMAT is free software; you can redistribute it and/or modify % it under the terms of the GNU General Public License as published % by the Free Software Foundation; either version 2 of the license, % or (at your option) any later version. % % UVMAT is distributed in the hope that it will be useful, % but WITHOUT ANY WARRANTY; without even the implied warranty of % MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the % GNU General Public License (see LICENSE.txt) for more details. %======================================================================= function DataOut=phys(DataIn,XmlData,DataIn_1,XmlData_1) %------------------------------------------------------------------------ % A FAIRE: 1- verifier si DataIn est une 'field structure'(.ListVarName'): % chercher ListVarAttribute, for each field (cell of variables): % .CoordType: 'phys' or 'px' (default==phys, no transform) % .scale_factor: =dt (to transform displacement into velocity) default=1 % .covariance: 'scalar', 'coord', 'D_i': covariant (like velocity), 'D^i': contravariant (like gradient), 'D^jD_i' (like strain tensor) % (default='coord' if .Role='coord_x,_y..., % 'D_i' if '.Role='vector_x,...', % 'scalar', else (thenno change except scale factor) DataOut=[]; DataOut_1=[]; %default second output field if isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0) if isfield(XmlData,'GeometryCalib')&& isfield(XmlData.GeometryCalib,'CoordUnit') DataOut.CoordUnit=XmlData.GeometryCalib.CoordUnit;% states that the output is in unit defined by GeometryCalib, then erased all projection objects with different units end return end %% analyse input and set default output DataOut=DataIn;%default first output field if nargin>=2 % nargin =nbre of input variables if isfield(XmlData,'GeometryCalib') Calib{1}=XmlData.GeometryCalib; else Calib{1}=[]; end if nargin>=3 %two input fields DataOut_1=DataIn_1;%default second output field if nargin>=4 && isfield(XmlData_1,'GeometryCalib') Calib{2}=XmlData_1.GeometryCalib; else Calib{2}=Calib{1}; end end end %% get the z index defining the section plane if isfield(DataIn,'ZIndex')&&~isempty(DataIn.ZIndex)&&~isnan(DataIn.ZIndex) ZIndex=DataIn.ZIndex; else ZIndex=1; end %% transform first field iscalar=0;% counter of scalar fields if ~isempty(Calib{1}) if ~isfield(Calib{1},'CalibrationType')||~isfield(Calib{1},'CoordUnit') return %bad calib parameter input end if ~(isfield(DataIn,'CoordUnit')&& strcmp(DataIn.CoordUnit,'pixel')) return % transform only fields in pixel coordinates end DataOut=phys_1(DataIn,Calib{1},ZIndex);% transform coordinates and velocity components %case of images or scalar: in case of two input fields, we need to project the transform on the same regular grid if isfield(DataIn,'A') && isfield(DataIn,'Coord_x') && ~isempty(DataIn.Coord_x) && isfield(DataIn,'Coord_y')&&... ~isempty(DataIn.Coord_y) && length(DataIn.A)>1 iscalar=1; A{1}=DataIn.A; end end %% document the selected plane position and angle if relevant if isfield(Calib{1},'SliceCoord')&&size(Calib{1}.SliceCoord,1)>=ZIndex DataOut.PlaneCoord=Calib{1}.SliceCoord(ZIndex,:);% transfer the slice position corresponding to index ZIndex if isfield(Calib{1},'SliceAngle') % transfer the slice rotation angles if isequal(size(Calib{1}.SliceAngle,1),1)% case of a unique angle DataOut.PlaneAngle=Calib{1}.SliceAngle; else % case of multiple planes with different angles: select the plane with index ZIndex DataOut.PlaneAngle=Calib{1}.SliceAngle(ZIndex,:); end end end %% transform second field if relevant if ~isempty(DataOut_1) if isfield(DataIn_1,'ZIndex') && ~isequal(DataIn_1.ZIndex,ZIndex) DataOut_1.Txt='different plane indices for the two input fields'; return end if ~isfield(Calib{2},'CalibrationType')||~isfield(Calib{2},'CoordUnit') return %bad calib parameter input end if (isfield(DataIn_1,'CoordUnit')&& strcmp(DataIn_1.CoordUnit,'pixel')) DataOut_1=phys_1(DataOut_1,Calib{2},ZIndex); end if isfield(Calib{1},'SliceCoord') if ~(isfield(Calib{2},'SliceCoord') && isequal(Calib{2}.SliceCoord,Calib{1}.SliceCoord)) DataOut_1.Txt='different plane positions for the two input fields'; return end DataOut_1.PlaneCoord=DataOut.PlaneCoord;% same plane position for the two input fields if isfield(Calib{1},'SliceAngle') if ~(isfield(Calib{2},'SliceAngle') && isequal(Calib{2}.SliceAngle,Calib{1}.SliceAngle)) DataOut_1.Txt='different plane angles for the two input fields'; return end DataOut_1.PlaneAngle=DataOut.PlaneAngle; % same plane angle for the two input fields end end if isfield(DataIn_1,'A')&&isfield(DataIn_1,'Coord_x')&&~isempty(DataIn_1.Coord_x) && isfield(DataIn_1,'Coord_y')&&... ~isempty(DataIn_1.Coord_y)&&length(DataIn_1.A)>1 iscalar=iscalar+1; Calib{iscalar}=Calib{2}; A{iscalar}=DataIn_1.A; end end %% transform the scalar(s) or image(s) if iscalar~=0 [A,Coord_x,Coord_y]=phys_ima(A,XmlData,ZIndex);%TODO : introduire interp2_uvmat ds phys_ima if iscalar==1 && ~isempty(DataOut_1) % case for which only the second field is a scalar DataOut_1.A=A{1}; DataOut_1.Coord_x=Coord_x; DataOut_1.Coord_y=Coord_y; else DataOut.A=A{1}; DataOut.Coord_x=Coord_x; DataOut.Coord_y=Coord_y; end if iscalar==2 DataOut_1.A=A{2}; DataOut_1.Coord_x=Coord_x; DataOut_1.Coord_y=Coord_y; end end % subtract fields if ~isempty(DataOut_1) DataOut=sub_field(DataOut,[],DataOut_1); end %------------------------------------------------ %--- transform a single field function DataOut=phys_1(Data,Calib,ZIndex) %------------------------------------------------ %% set default output DataOut=Data;%default DataOut.CoordUnit=Calib.CoordUnit;% the output coord unit is set by the calibration parameters %% transform X,Y coordinates for velocity fields (transform of an image or scalar done in phys_ima) if isfield(Data,'X') &&isfield(Data,'Y')&&~isempty(Data.X) && ~isempty(Data.Y) [DataOut.X,DataOut.Y]=phys_XYZ(Calib,Data.X,Data.Y,ZIndex); Dt=1; %default if isfield(Data,'dt')&&~isempty(Data.dt) Dt=Data.dt; end if isfield(Data,'Dt')&&~isempty(Data.Dt) Dt=Data.Dt; end if isfield(Data,'U')&&isfield(Data,'V')&&~isempty(Data.U) && ~isempty(Data.V) [XOut_1,YOut_1]=phys_XYZ(Calib,Data.X-Data.U/2,Data.Y-Data.V/2,ZIndex); [XOut_2,YOut_2]=phys_XYZ(Calib,Data.X+Data.U/2,Data.Y+Data.V/2,ZIndex); DataOut.U=(XOut_2-XOut_1)/Dt; DataOut.V=(YOut_2-YOut_1)/Dt; end end %% suppress tps list_tps={'Coord_tps' 'U_tps' 'V_tps' 'SubRange' 'NbSites'}; ind_remove=[]; for ilist=1:numel(list_tps) ind_tps=find(strcmp(list_tps{ilist},Data.ListVarName)); if ~isempty(ind_tps) ind_remove=[ind_remove ind_tps]; DataOut=rmfield(DataOut,list_tps{ilist}); end end if isfield(DataOut,'VarAttribute') && numel(DataOut.VarAttribute)>=3 && isfield(DataOut.VarAttribute{3},'VarIndex_tps') DataOut.VarAttribute{3}=rmfield(DataOut.VarAttribute{3},'VarIndex_tps'); end if isfield(DataOut,'VarAttribute')&& numel(DataOut.VarAttribute)>=4 && isfield(DataOut.VarAttribute{4},'VarIndex_tps') DataOut.VarAttribute{4}=rmfield(DataOut.VarAttribute{4},'VarIndex_tps'); end if ~isempty(ind_remove) DataOut.ListVarName(ind_remove)=[]; DataOut.VarDimName(ind_remove)=[]; DataOut.VarAttribute(ind_remove)=[]; end %% transform of spatial derivatives: TODO check the case with plane angles if isfield(Data,'X') && ~isempty(Data.X) && isfield(Data,'DjUi') && ~isempty(Data.DjUi) % estimate the Jacobian matrix DXpx/DXphys for ip=1:length(Data.X) [Xp1,Yp1]=phys_XYZ(Calib,Data.X(ip)+0.5,Data.Y(ip),ZIndex); [Xm1,Ym1]=phys_XYZ(Calib,Data.X(ip)-0.5,Data.Y(ip),ZIndex); [Xp2,Yp2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)+0.5,ZIndex); [Xm2,Ym2]=phys_XYZ(Calib,Data.X(ip),Data.Y(ip)-0.5,ZIndex); %Jacobian matrix DXpphys/DXpx DjXi(1,1)=(Xp1-Xm1); DjXi(2,1)=(Yp1-Ym1); DjXi(1,2)=(Xp2-Xm2); DjXi(2,2)=(Yp2-Ym2); DjUi(:,:)=Data.DjUi(ip,:,:); DjUi=(DjXi*DjUi')/DjXi;% =J-1*M*J , curvature effects (derivatives of J) neglected DataOut.DjUi(ip,:,:)=DjUi'; end DataOut.DjUi = DataOut.DjUi/Dt; % min(Data.DjUi(:,1,1))=DUDX end %%%%%%%%%%%%%%%%%%%%